In a video shared on the official Twitter handle of Khan's ruling Pakistan Tehreek-e-Insaf (PTI), the cricketer-turned-politician is seen sitting while other leaders and dignitaries stood to welcome various heads of states arriving in the hall on Thursday.
He stood briefly when his name was announced and then seated himself again before the others did in a breach of protocol.
Khan was trolled online by the netizens for the gaffe after the video went viral.
"Must study the decorum of diplomatic visits to make some mark in future Mr Imran Khan," one Twitter user wrote.
"This man has been installed as PM by the establishment. They can't make him a statesman. He doesn't even know the ABC of diplomacy," said another user.
"He may be thinking of his next marriage. Hence absent minded," tweeted another.
This was not the first time Khan made a faux pax at an international forum. He earlier broke the diplomatic protocol at the 14th Organisation of Islamic Cooperation (OIC) summit held in Saudi Arabia earlier this month.
During his brief encounter with the Saudi King Salman bin Abdulaziz on the sidelines of the summit, Khan angered Saudi netizens when he walked away after speaking to King Salman's translator without waiting for the message to be translated to the king.
( With inputs from IANS )