Kenya has suspended the licences of 13 Somali remittance firms following the assault on a college by al-Shabab fighters killing more than 200 people.
The April 2 attack in Garissa, 200km from the Somalia border, was Kenya's deadliest since al-Qaeda bombed the US embassy in 1998.
Bashir Issa Ali, Somalia's central bank governor, said on Wednesday that money-transfer firms in the country had been officially notified by Central Bank of Kenya (CBK) about the closure of accounts.
He said the move would have a devastating impact Kenya's Somali community, numbering just over one million people, the Reuters news agency reported.
The killing of 148 students by Somalia's al-Shabab has piled pressure on Kenya's President Uhuru Kenyatta to deal with the armed group, which has killed more than 400 people in Kenya in the last two years.
Kenyan media reported dozens of bank accounts had been frozen.
Kenya's Daily Nation newspaper said on Wednesday that the government has "frozen the accounts of 86 individuals and entities suspected to be financing terrorism in the country", including Somali remittance firms.
"It’s going to hurt Somalis in Kenya more than Somalis in Somalia. The amount of money sent from abroad to Kenya is huge," Ali said, pointing out that many Somalis in Kenya rely on relatives abroad for basics including school fees.
On Tuesday, Amina Mohamed, Kenya's foreign minister, said Kenya is seeking additional foreign intelligence and security help after the Garissa massacre.