Foreign ministry spokesman Ilyas Omarov said: "We never delivered any weapons to that country."
He said that Kazakhstan was "strictly" following the UN-imposed embargo on arms supplies to Somalia.
But witnesses said an Ilyushin-76 (Il-76) cargo plane, with the Kazakh flag painted on its tail, landed in the country's capital on July 26 and 28.
The embattled Somali government said the flights were delivering weapons, including land mines and long-range guns, from neighboring Eritrea to support the Supreme Islamic Courts.
Both the Islamists and Eritrean officials have denied the accusation.
Kazakhstan's National Security Committee said last week that it was investigating the reports.
The Kazakh Civil Aviation Committee said that officially no Kazakh Il-76 is being leased by any African state or company.
It also said that no Kazakh Il-76 has been ever been sold to a client in Africa.
It also said that there are 16 Il-76s operated by five Kazakh companies that carry the country's national insignia, and all those companies were being investigated.
Since the 1991 collapse of the Soviet Union, Kazakh officials have been involved in a string of illegal arms scandals.
These included sales of MiG fighters to South Korea, and other military equipment and weapons to North Korea, Ethiopia, Congo and other countries.