Leader of the House Christopher Pyne says he did not give MPs permission to leave Parliament early, labelling a series of embarrassing defeats for the government in the House of Representatives on Thursday a "stuff up".

The chaotic end to the first week of the new Parliament has triggered a blame game and Justice Minister Michael Keenan on Friday took responsibility for his absence, saying "it was a work-related matter but that's obviously no excuse".

The government, commanding a slim majority with 76 seats, lost multiple procedural votes as senior ministers Peter Dutton, Christian Porter and Mr Keenan were absent from the chamber.

On Friday, Mr Pyne attempted to insulate himself from blame as the ministers and government whips – responsible for rallying and counting MPs for votes – also face serious questions over the events.