Khan said a group of students from the hardline Jamaat-e-Islami party had collaborated with the police to arrest him.
"I am very worried and angry - Musharraf should realise that we don't need him"
Avas, Islamabad, Pakistan
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Kamal Hyder, Al Jazeera's correspondent in Islamabad, said the Pakistani federal government has not yet confirmed that Khan was being booked under the anti-terrorism act.
"A government official told us this was a provincial issue and therefore that it is possible it could have happened at that level, but the government was not willing to confirm or deny the reports."
"If indeed the government does confirm that this has happened then Imran Khan is being tried by a very serious court, which is the anti-terrorist court."
Khan had been in hiding for 12 days after Musharraf declared emergency rule.
Khan's arrest came after the US said it was sending its number two diplomat to Pakistan to urge Musharraf to end emergency rule.
John Negroponte, the US deputy secretary of state, is expected during his visit on Friday to push for a return to constitutional rule and for free and fair elections to be held.
The move comes amid upheaval in Pakistan following the imposition of a state of emergency by Musharraf in early November, leading to the suspension of the constitution, sacking of the chief judge and a crackdown on the media.
Tom Casey, the US deputy state department spokesman, said on Wednesday: "I would expect that he will provide the same message in private to Pakistani officials that we have been saying in public.
"We want to see all moderate political forces be able to work together. We continue to want to see elections move forward in a free, fair and transparent manner [and] we want to see the emergency decree lifted."
In a separate development, the leaders of Pakistan's two main opposition parties are reported to be working to form an alliance.
The proposed pact was revealed by Benazir Bhutto, a former prime minister and head of the Pakistan Peoples' Party, who remains under house arrest in her Lahore residence.
Bhutto has called on Musharraf to step down as president and said she is seeking a partnership with Nawaz Sharif, her long-time rival and the exiled leader of the Pakistan Muslim League.
She said: "[Musharraf] must quit as president and as chief of army staff.
"I call on the international community to stop backing ... the man whose dictatorship threatens to engulf this nuclear-armed state in chaos," she said.
She also said for the first time that she would not serve under Musharraf should he win the elections he has promised by January 9.
"I would not serve as prime minister under a man who has repeatedly broken his promises, who is a dictator," said Bhutto, who has previously held talks with Musharraf on sharing power.
On Wednesday, Sharif said he was ready to work with Bhutto, against Musharraf.
"We are ready to set aside our differences with the People's Party and work for the return of democratic rule," Sharif said by telephone from Saudi Arabia, referring to Bhutto's party.
Asked whether there was any possibility of a broad opposition coalition against Musharraf, Sharif said: "It's the need of the hour.
"There is no room for dictatorship in Pakistan. We don't accept this set-up," he said.
Musharraf meanwhile spent the day in a series of interviews aimed at defending his decision to impose emergency rule. He said emergency rule would stay in place until after the elections.
"Emergency is not meant to rig elections," he said. "Emergency is in fact meant to make sure that the elections are held in a peaceful manner.
"The issue of transparency; We are inviting any amount of observers to Pakistan to see [the election]. Let them come and see the transparency of the election," he said.
"What the the oppositon is talking about is agitation. They want to disturb law and order and undermine governance."
Source: Al Jazeera and agencies