Mahara, a senior member of the ruling Nepal Communist Party and former Maoist rebel, denied the allegation but stepped down as speaker last week after the woman gave details of the assault to media
Police have arrested the former speaker of Nepal's parliament after a female employee in the assembly accused him of rape.
A police van arrived at Krishna Bahadur Mahara's residence late Sunday and took him into custody after the district court ordered his arrest.
"He was taken into custody yesterday to investigate the case," Shyam Lal Gyawali, Kathmandu police spokesman told AFP.
Mahara, a senior member of the ruling Nepal Communist Party and former Maoist rebel, denied the allegation but stepped down as speaker last week after the woman gave details of the assault to media.
The communist government had faced mounting pressure over the case.
In a video interview published by the hamrakura.com news website on Monday, the woman said Mahara was drunk when he arrived at her home on September 29. He persuaded her to drink alcohol before assaulting her.
"I had not thought it would come to this. He forced himself on me he left after I said I will call the police," she said in the interview.
The woman showed apparent bruises on her arms, hands and feet.
Police said they went to her home the same night, but she did not file a case straight away.
Investigators collected evidence including a bottle of whisky and a pair of broken spectacles, allegedly belonging to Mahara, police said.
However, the woman withdrew her allegation in mid-week, following what many were threats and pressure, media reports said. The woman eventually filed a formal complaint on Friday.
The government faced intense public pressure to make sure the woman's accusations were acted on.
On Friday, the United Nations and foreign embassies in Nepal issued a joint statement urging the government to act against violence against women, without specific reference to Mahara.
"The undersigned call upon all relevant state authorities to send a clear message of zero tolerance to any forms of gender-based violence by anyone under any circumstances," the statement read.
A former rebel leader during Nepal's decade-long Maoist insurgency, Mahara has previously served as deputy prime minister and has held several ministerial posts.