Bangladesh on Sunday summoned Pakistan's acting high commissioner to protest its interference in its affairs after Islamabad said it was "deeply saddened" by the execution of a top Islamist party figure for atrocities committed during the war to leave Pakistan.

Mir Quasem Ali, 63, a key financier of the Jamaat-e-Islami party, was executed on Saturday at Kashimpur Central Jail on the outskirts of the capital, for murder, confinement, torture and incitement to religious hatred during the war.

Pakistan's foreign ministry said it was "deeply saddened" by Ali's execution, describing the proceedings of the war tribunal as "flawed".

Since December 2013 five prominent Jamaat members, including Ali, and a leader of the main opposition party, have been executed for war crimes.

Relations between the two countries have never recovered from the 1971 war when Bangladeshi nationalists, backed by India, broke away from what was then West Pakistan.

Official figures show about 3 million people were killed and thousands of women were raped during the war, in which some factions, including the Jamaat-e-Islami, opposed the breakaway. The party denies that its leaders committed any atrocities.

"By repeatedly taking the side of those Bangladesh nationals who are convicted of crimes against humanity and genocide, Pakistan has once again acknowledged its direct involvement and complicity with the mass atrocity crimes committed during Bangladesh’s Liberation War in 1971," Bangladesh said in a statement.

"The Government of Bangladesh strongly rejects Pakistan’s claim that these are ‘recriminations for political gains’."

Critics say Prime Minister Sheikh Hasina has used the war crimes tribunal, set up in 2010, to target Jamaat and weaken the opposition. The government denies the accusations.

International human rights groups say the tribunal's procedures fall short of international standards but Bangladesh rejects that and the trials are supported by many Bangladeshis.

In January, a Bangladeshi diplomat in Pakistan was expelled in what Dhaka officials called "an act of retaliation" after a Pakistani diplomat in Dhaka was expelled for spying.