Speaking to the press in Karlovac, Sanader said that if Bosnia failed to respect the agreement and the European standards it aspired to, Croatia would take countermeasures to protect its economy.
He was commenting on announcements that Bosnia might introduce new tariffs on some Croatian products.
Sanader said that those aspiring to join the EU must apply European standards and that the Bosnian government was not doing so.
He added he understood the Bosnian government's concern about the high foreign trade deficit, but said Croatia too had a high deficit with some countries, yet was not taking the measures Bosnia had decided on.
Sanader said he bound Agriculture Minister Petar Cobankovic to discuss the issue with his Bosnian counterpart.
In March, Bosnia unilaterally introduced tariffs on milk, dairy products, meat and meat products from Croatia, although this was contrary to their free trade agreement.
Citing unofficial sources, Croatian and Bosnian media have said that the Bosnian government is allegedly considering protective measures for the import of coffee, cigarettes, oil and other high-tariff goods from Croatia.