"We prevented Mohammed al-Daini from flying to Amman today because there is an order from the judiciary to prevent him from leaving Iraq," ministry spokesman General Abdel Karim Khalaf told AFP.
But Daini, an Arab MP who has insisted on his innocence, was not arrested at Baghdad airport as he still had parliamentary immunity.
The deputy has dismissed charges of having ordered the bombing in which eight people died including a fellow MP as a politically motivated "fabrication" due to his party's defence of human rights.
"We have been disclosing serious violations of human rights in Iraqi prisons," Daini, a member of the National Dialogue Front, told journalists earlier this week.
"We knew there would be a price to pay ... but we didn't expect it to go this far, to go beyond all constitutional and legal norms," he said.
"These are fabrications ... It was clear they were tortured when they were shown on television," the MP said, referring to video recordings of two of his bodyguards confessing to being involved in the suicide bombing.
The MP, an ex-member of an elite Saddamist force, was accused on Sunday of ordering the April 2007 bombing in the parliament's canteen.
Reporters were shown the confessions -- also broadcast on television -- by a nephew and a security guard of the accused MP who said they had carried out several attacks for Daini.
"The suicide bomber entered with an authorisation paper from Mohammed al-Daini and blew himself up at the parliament," nephew Riad Ibrahim al-Daini said on the video, adding that he had taken the assailant to the scene.
Major General Qassem Atta, spokesman for Baghdad's military security command, has told reporters the MP's immunity has not yet been lifted but a request made to the judicial authorities.