The two bodies are “highly likely” to be two of the attackers, an official said.
Ndung’u Gethenji, chairman of the committee investigating the attack, said AK47 rifles used by the militants were found next to the bodies.
The authorities will now conduct forensic tests on the bodies.
At least 67 people died when suspected al-Shabab militants stormed the Nairobi shopping centre on 21 September.
The attack sparked a four-day siege in which large parts of the shopping centre were destroyed.
The Kenyan authorities have released the names, or nicknames, of four suspects in the attack, but have given few other details.
Ndung’u Gethenji said the bodies recovered on Thursday were likely to be militants because the army does not use AK47s.
He said another body recovered from the rubble was likely to be a soldier.
It is still not clear whether some of the attackers might have escaped, or even how many attackers there were.
Officials initially said 10 to 15 gunmen were involved, but CCTV footage appears to show only four militants.
The Somali militant group al-Shabab said its members carried out the attack in response to Kenya’s army carrying out operations on Somali territory.
There are about 4,000 Kenyan troops in the south of Somalia, where they have been fighting the militants since 2011.
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