Last month, Spain's regional government approved the creation of the ministry and made Raul Romeva its head.
"There is a conflict of jurisdictions there," Catala said at a press conference.
He added that the decision of the Catalan government "is contrary to the law" since only the central government can direct Spanish foreign policy.
The secessionist motion in the Catalan parliament was facilitated by the victory of the pro-independence Catalan Junts pel Si (Together for Yes) coalition and their allies from the left-wing Popular Unity Candidacy (CUP) in the regional election in September. The broad coalition secured 72 seats in the 135-member regional parliament.