Julius Karangi said that a third soldier was under investigation.
He has previously said that soldiers had only taken water during the four-day siege, despite CCTV footage seeming to show them helping themselves to goods in a supermarket.
Somali Islamist group al-Shabab says it was behind the attack, which killed 67.
At the same news conference, Police Criminal Investigation Department head Ndegwa Muhoro said that a phone call had been made to Norway during the siege.
One of the suspected attackers has been named as 23-year-old Somalia-born Norwegian national, Hassan Abdi Dhuhulow.
The Kenyan army has said that all four of the attackers died.
Ndegwa Muhoro said that Interpol was helping to analyse the bodies to confirm their identities, reports the AFP news agency.
Officials had initially said there were 10-15 attackers.
Ndegwa Muhoro said that five other people were in detention over the attack and would be charged soon.
Several shop-owners have said that their premises were looted during the siege.
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