The Foreign Office in a statement said that Pakistan protested over the "use of undiplomatic language in a Note Verbale, on an incident of obscure origin."
"The High Commissioner was conveyed that sharing of a video by a third party cannot be attributed to Pakistan High Commission in Dhaka, the foreign office said.
Bangladesh yesterday demanded an apology from Pakistan after its envoy in Dhaka posted a video claiming that the country's founder Sheikh Mujibur Rahman was not the one who declared its independence in 1971.
The Pakistani mission in Dhaka shared the video on its Facebook page, sparking a controversy that prompted it to remove the post.
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The Foreign Office said Pakistan has been pursuing a policy of maintaining friendly and cordial ties with Bangladesh.
"Pakistan desires to move forward in accordance with the Tripartite Agreement of 1974 wherein the Prime Minister of Bangladesh desired that the people of Bangladesh should 'forget the past and make a fresh start', it said.
"Let me clarify that the video clip was uploaded not on our website, but on the High Commissions Facebook page by someone else. The video was immediately deleted, and we have tweeted about it from Spokespersons official account yesterday, he said.
Bangladesh emerged as an independent nation, breaking away from Pakistan after its victory in the 1971 liberation war aided by India.
Bilateral relations have suffered in recent years over the 1971 war crimes trial in Bangladesh and executions of former Bengali war criminals who colluded with the invading Pakistani troops.