The blasts come at a time of rising militant violence and deepening political uncertainty in Pakistan, with the army chief and president, General Pervez Musharraf, preparing to try to secure a new term and his opponents vowing to end his rule.
The government dismissed speculation the blasts could lead to declaration of an emergency and postponement of presidential and parliamentary elections due in coming weeks and months.
There was no claim of responsibility but the Interior Ministry said evidence pointed to Al Qaeda-linked militants who are battling security forces near the Afghan border.
One bomb blew up a bus carrying Defence Ministry staff about a kilometre (half a mile) from army headquarters, said military spokesman Major-General Waheed Arshad.
The second went off in a market area of Rawalpindi, the sister city of Islamabad where Musharraf and many other top military officials live and where Islamabad’s international airport is located.
‘Both were suicide bombings but I have no detail about how they were carried out,’ Arshad said.
Both went off at around 7:20 a.m. (0220 GMT).
Earlier, some officials said the staff on the bus were from an agency involved in atomic work, while others said they were from a security agency.
‘The bus was totally packed. I saw 15 to 20 mutilated bodies,’ said Tanveer Ahmed, a government employee waiting for another bus near the spot, quickly cordoned off by soldiers.
The body and roof of the bus were almost totally blown away. Pieces of flesh and strips of clothing hung limply from the twisted metal frame as rescuers struggled to pull out the dead.
Pakistan has suffered a surge of militant violence since July, when commandos stormed a radical mosque in Islamabad and a peace pact broke down with militants in the North Waziristan region on the Afghan border.
While most of the violence has been in the northwest, there were two suicide bomb attacks in Islamabad in July.
Musharraf issued a statement condemning the latest blasts.
Deputy Information Minister Tariq Azim Khan said a suicide bomber had apparently managed to board the bus that was blown up.
‘Anyone who thinks they can destabilise Pakistan will be disappointed. There will be no derailment. Elections will be on time,’ Khan told Reuters.
Police initially said the second blast, also close to army headquarters, was caused by a bomb on a motorcycle. Several parked cars along the road and nearby shops were badly damaged.
Arshad said he could not give a breakdown of how many were killed on the bus and how many by the second blast but other officials said more people were killed in the bus blast.
Interior Ministry spokesman Javed Iqbal Cheema said the blasts were part of a pattern of attacks.
‘You know what is going on in the tribal areas, it is an extension of that,’ he said, referring to semi-autonomous tribal lands on the Afghan border where Al Qaeda and and pro-Taleban militants are battling security forces.
Taleban militants in neighbouring Afghanistan, who are allied with militants in Pakistan, have carried out several similar attacks on buses carrying government employees to work in the Afghan capital.