"In circumstances when the nation is facing most sensitive times, a change of the top nuclear negotiator is not in line with the national interests and the good of the system," said a letter signed by 23 MPs.
"It was necessary for the president to act with more tolerance and thought," said the statement addressed to Ahmadinejad, quoted by the Fars news agency.
Fars said that the letter had been signed by 22 MPs from parliament's reformist minority and also by one conservative.
Iran last week announced the resignation of the relative moderate Larijani as top nuclear negotiator and his replacement by Saeed Jalili, a close ally of the president.
One hundred and sixty-seven MPs from across the conservative-dominated parliament last week signed a letter hailing Larijani's "valuable efforts" on the nuclear issue even if they stopped short of outright criticism of his departure.
There have already been complaints from the media and officials this was the wrong time for such a high level change. Even the foreign policy advisor to supreme leader Ayatollah Ali Khamanei said Larijani should not have quit.
Larijani had fallen out with Ahmadinejad over how to handle the Iranian nuclear dossier and had offered his resignation on several previous occasions.
However Larijani still attended talks with EU foreign policy chief Javier Solana in Rome alongside his successor, raising questions amongst observers about who was really in charge.
But foreign ministry spokesman Mohammad Ali Hosseini insisted that there was complete unity between Iranian officials over the nuclear issue.
"This round of talks (in Rome) with Mr Larijani and Mr Jalili was good and constructive and it showed the unified stance taken by our nation's officials."