Quoting a senior security source, the newspaper on Wednesday said the six Pakistanis had entered Egyptian territory on 5 July and checked into a hotel in the southern Cairo suburb of Maadi, where their passports were later found.
Cairo later said the six were not suspects in the deadly 23 July attacks.
"We know they never went to Sharm al-Shaikh," the source told Al-Ahram.
Egyptian security sources had said two days after Egypt's deadliest ever attacks that six Pakistanis were suspected of links to the bombings.
The news had increased the pressure on Pakistan, following the deadly 7 July bombings in London, where three of the bombers were of Pakistani origin and are suspected of ties with Osama bin Laden's al-Qaida network.
But on Tuesday, the Egyptian embassy in Pakistan said the authorities in Cairo had never accused any Pakistani national of involvement in the 23 July attacks which according to the Health Ministry left at least 67 people dead.
"The information we have points to the fact that they trekked through the desert and headed towards Israel"
Egyptian security source
Said Abd al-Fattah, manager of the Sharm al-Shaikh International hospital where the victims were taken, said 88 people were killed.
At least 119 people were also wounded, Egypt's Interior Ministry has said.
Pictures of five of the six suspected Pakistanis had been posted in police stations in Cairo and in the Sharm al-Shaikh area.
"Their pictures had been published on 9 July (before the Sharm attacks), because they suddenly disappeared from the hotel, leaving their passports behind," the security official was quoted as saying.
"The information we have points to the fact that they trekked through the desert and headed towards Israel," he added.
Egypt's arid Sinai peninsula is a major route for thousands of illegal immigrants seeking jobs in Israel, often with the assistance of beduin desert trackers.