In the latest of a series of controversies to engulf Pakistan, the pair face bans of up to two years if a second test confirms the results, Pakistan Cricket Board director of operations Salim Altaf said on Monday.
"I can confirm that Shoaib Akhtar and Mohammad Asif have tested positive for the performance-enhancing anabolic steroid nandrolone and they have been called back to Pakistan", Altaf told AFP.
The PCB conducted its own internal tests on 25 players before the Champions Trophy in India and the samples were sent to an accredited lab in Malaysia, which informed the board about the two positive tests, he said.
"Now we have asked them for a second test or 'B sample'."
Pakistan has no current system for doping offences but will set up a tribunal to decide how to punish Akthar and Asif if their test results are confirmed, the PCB official said.
"But we know that it's a big issue and under the ICC (International Cricket Council) anti-doping rules the punishment for a first violation is two years," Altaf added.
"The whole issue is very sad and disappointing".
Altaf however denied earlier reports that fellow paceman Rana Naved-ul-Hasan's test had raised questions.
Pakistan coach Bob Woolmer appeared stunned when he faced a televised press conference in Jaipur, India, where Pakistan face Sri Lanka in their opening Champions Trophy match on Tuesday.
"What was my initial reaction? Disappointment," the English-born Woolmer said.
"We asked the (PCB) medical panel to give the players drug tests which they did at the end of September, so I take responsibility for that certainly," the English-born coach added.
"I have never come across anything like this in my life.... The timing is not great, but if it's going to happen it happens."
Captain Younis Khan added: "Sometimes people take something and it comes out in the test."
Pakistan is lining up fast bowlers Mohammad Sami and Shahid Nazir and all-rounder Yasir Arafat to fly out to India as soon as possible, a board official told AFP on condition of anonymity.
Recently-appointed PCB chairman Nasim Ashraf was due to give an official announcement at a press conference here at 3:00 pm (1000 GMT) following an urgent board meeting.
The tests rob Pakistan of two key elements of its strike force and follow two months of controversy swirling around the squad.
The chaos started in the fourth Test against England at the Oval in August, when captain Inzamam-ul Haq refused to take his team back on the field after it was accused of ball-tampering.
Inzamam was cleared of that charge but was still handed a four-match ban for bringing the game into disrepute.
His replacement Younis earlier this month refused to lead the side for the Champions Trophy, saying he did not want to be a "dummy" captain.
Then-PCB chief Shaharyar Khan quit the next day because of his decision. Khan's replacement Ashraf reinstated Younis as skipper.
Former Pakistan skipper Rashid Latif told AFP said the positive tests were a major setback for Pakistan but praised the cricket board for taking prompt action.
"Never before has any Pakistani player tested positive and it's most serious," Latif said. "It's a setback for Pakistan and a most serious crisis, but it's a bold decision by the PCB."