Pakistan High Commissioner Shuja Alam was summoned, a foreign ministry spokesman here said but declined to elaborate immediately.
The Pak envoy, emerging from the office of the acting foreign secretary Mohammad Khurshid Alam's office, told reporters he was asked about the incident in which a Bangladesh High Commission official in Islamabad went missing.
"I have been informed of yesterday's incident and I will convey the details to the (Bangladesh) foreign ministry after discussions with the Islamabad authorities," he said.
Bangladesh foreign ministry officials earlier said the personal officer of a Bangladeshi diplomat in Islamabad had gone missing but returned home "unhurt" early this morning.
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"Our High Commissioner in Islamabad briefly talked to Jahangir Hossain (who went missing). We are trying to know the details of what actually happened to him," a foreign ministry spokesman told PTI.
He said Hossain had left the office to pick his daughter before going home but went missing as he stepped out of the High Commission and his cell phone too remained switched off.
But the Pakistan High Commission said in a statement that
it noticed "a disturbing pattern of harassment of its officers and officials, followed by a mud-slinging campaign and media trial".
It said Bangladesh Police and security agencies were accusing the Pakistani mission staffers of having links to militants.
Diplomatic sources in Dhaka said Hossain's 'brief detention' seemed to be a counter action to what happened in Dhaka the same day.
The developments came a month after Islamabad withdrew a woman diplomat posted in Dhaka amid an uproar over her suspected links to Islamist terrorists nearly 12 months after Bangladesh expelled another Pakistani on identical charges.
Dhaka-Islamabad ties began to be strained since 2013 after Pakistan passed a national assembly resolution protesting execution of Jamaat-e-Islami's former Assistant Secretary General Abdul Quader Mollah over the war crimes charges.
The bilateral relations witnessed further strains two months ago over Pakistan's sharp reactions following executions of another two major 1971 war crimes convicts Salahuddin Quader Chowdhury and Ali Ahsan Mohammad Mojaheed, who were found guilty of carrying out atrocities during the liberation war against Pakistan.