Ministers agreed to send 6,500 new and used automatic rifles and some 7 million rounds of ammunition to Iraq via the U.S. government, and a separate shipment of ammunition to Jordan.
"The fight against Islamic State is an important part of solving the migration crisis that is hitting Europe," Sobotka said in a statement.
The NATO member has already supplied guns and ammunition to Kurdish forces in Iraq fighting insurgents, and agreed last year to sell surplus subsonic fighter jets to the Iraqi government.
The Czechs and their central European peers have stressed strong border protection and ending conflicts in the Middle East as the main way to solving Europe's worst migration crisis since World War Two and have refused to accept European Union quotas for distributing migrants.
(Reporting by Jason Hovet; Editing by Catherine Evans)