In fact, the Genocidal atmosphere had been created from that partition of British India in 1947. The Dominion of Pakistan comprised two geographically and culturally separate areas to the east and the west with India in between. The western zone was popularly (and for a period, also officially) termed West Pakistan and the eastern zone (modern-day Bangladesh) was initially termed East Bengal and later, East Pakistan. Although 56% of the total population was from Bengal, political power was concentrated in West Pakistan and it was widely perceived that East Pakistan was being exploited economically, leading to many grievances. Administration of two discontinuous territories was also seen as a challenge. 
In 1948, Governor-General Muhammad Ali Jinnah declared that "Urdu, and only Urdu" would be the federal language of Pakistan. However, Urdu was historically prevalent only in the north, central, and western region of the subcontinent; whereas in East Bengal, the native language was Bengali, one of the two most easterly branches of the Indo-European languages. The government stand was widely viewed as an attempt to suppress the culture of the eastern wing. The people of East Bengal demanded that their language be given federal status alongside Urdu and English. The Language Movement began in 1948, as civil society protested the removal of the Bengali script from currency and stamps, which were in place since the British Raj. The movement reached its climax in 1952, when on 21 February, the police fired on protesting students and civilians, causing several deaths.
Although East Pakistan had a larger population, West Pakistan dominated the divided country politically and received more money from the common budget.
|Year||Spending on West Pakistan (in millions of Pakistani rupees)||Spending on East Pakistan (in millions of Pakistani rupees)||Amount spent on East as percentage of West|
|Source: Reports of the Advisory Panels for the Fourth Five Year Plan 1970–75, Vol. I, |
published by the planning commission of Pakistan.
Bengalis were under-represented in the Pakistan military. Officers of Bengali origin in the different wings of the armed forces made up just 5% of overall force by 1965; of these, only a few were in command positions, with the majority in technical or administrative posts. West Pakistanis believed that Bengalis were not "martially inclined" unlike Pashtuns and Punjabis; the "Martial races" notion was dismissed as ridiculous and humiliating by Bengalis. Moreover, despite huge defense spending, East Pakistan received none of the benefits, such as contracts, purchasing and military support jobs. The Indo-Pakistani War of 1965 over Kashmir also highlighted the sense of military insecurity among Bengalis, as only an under-strength infantry division and 15 combat aircraft without tank support were in East Pakistan to thwart any Indian retaliations during the conflict. 
The only common bond between the two Pakistani wings was religion. But there were differences even in religious practices. Bengali Muslims tended to be less conservative in religious zeal, and had come to accept their Hindu minority and neighbors despite some communal clashes. Many Bengali Muslims strongly objected to the Islamist paradigm imposed by the Pakistani state. Most members of West Pakistan's ruling elite also belonged to a liberal society, yet understood a common faith as the mobilizing factor behind Pakistan's creation and the subsuming of Pakistan's multiple identities into one. 
Cultural and linguistic differences between the two wings outweighed any religious unity. The Bengalis were very proud of their culture and language which, with its Eastern Nagri script and Pali vocabulary, was unacceptable to the West Pakistani elite, who considered it to smack of Hindu culture.
The Bangladeshi liberation struggle against Pakistan was led by secular leaders.  With this reality and the feeling of Islamic solidarity in the background, Islamists in East Pakistan viewed Bengali nationalism as unacceptable and instead sided with the Pakistani Army's efforts to crush the Bengali independence movement.
From the very beginning of Pakistan, West Pakistan Establishment considered the East as their colony. They tried to oppress politics, economy, culture and history of Bengali Nation of the East Pakistan. Thus the ground of Genocide had been preparing from 24 years.
Finally its out broken when Awami League- The Bengali Nationalist Party ,Lead By Sheikh Mujibur Rahman won a landslide victory in the national elections. The party won 167 of the 169 seats allotted to East Pakistan, and thus a majority of the 313 seats in the National Assembly. This gave the Awami League the constitutional right to form a government. However, Zulfikar Ali Bhutto (a former Foreign 4 Minister and backed by Pakistan Army), the leader of the Pakistan Peoples Party, refused to allow Rahman to become the Prime Minister of Pakistan. That elicited outrage in the east wing, Awami league called for a non-cooperation movement from 3rd March 1971.
On 7th March Sheikh Mujibur Rahman delivered his historical speech where he urged his people to turn every house into a fort of resistance. He closed his speech saying, "Our struggle is for our freedom. Our struggle is for our independence." This speech is considered the main event that inspired the nation to fight for its independence. By this time mob clash were started between Bengali and migrated Bihari’s who were allies of Pakistan .
Between 10 and 13 March, Pakistan International Airlines cancelled all their international routes to urgently fly "government passengers" to Dacca. These "government passengers" were almost all Pakistani soldiers in civilian dress. MV Swat, a ship of the Pakistan Navy carrying ammunition and soldiers, was harbored in Chittagong Port, but the Bengali workers and sailors at the port refused to unload the ship. A unit of East Pakistan Rifles refused to obey commands to fire on the Bengali demonstrators, beginning a mutiny among the Bengali soldiers.
A planned military pacification carried out by the Pakistan Army – codenamed Operation Searchlight – started on 25 March 1971 to curb the Bengali independence movement by taking control of the major cities on 26 March, and then eliminating all opposition within one month. The Pakistani state claimed to justify starting Operation Searchlight on the basis of anti-Bihari violence by Bengalis in early March.
Before the beginning of the operation, all foreign journalists were systematically deported from East Pakistan. The main phase of Operation Searchlight ended with the fall of the last major town in Bengali hands in mid-May but then after military operations spread out to all over.
The operation also began the 1971 Bangladesh genocide. These systematic killings served only to enrage the Bengalis, which ultimately triggered Bangladesh Liberation War and creation of Independent Bangladesh by surrender of Pakistan army to Joint Force of Bangladesh ( MuktiBahini) & India at 16th December 1971.
References:1. http://www.kean.edu/~bgsg/Resources/background.htm . 2. "Demons of December – Road from East Pakistan to Bangladesh". Defencejournal.com . 3. Rounaq Jahan (1972). Pakistan: Failure in National Integration. Columbia University Press. ISBN 0-231-03625-6. Pg 166–167 4. "The events in East Pakistan, 1971: a legal study". ICJ.org . 5. Husain Haqqani (10 March 2010). Pakistan: Between Mosque and Military. Carnegie Endowment. pp. 19–. ISBN 978-0-87003-285-1. 6. Anne Noronha dos Santos (2007). Military Intervention and Secession in South Asia: The Cases of Bangladesh, Sri Lanka, Kashmir, and Punjab. p. 24. 7. Pakistan: From the Rhetoric of Democracy to the Rise of Militancy. Routledge. 2012. p. 168. 8. LINTNER, BERTIL (2004). "Religious Extremism and Nationalism in Bangladesh" (PDF). p. 418.