Additional checks by the police revealed that Moto stayed in Zagreb on March 19 and 20 and that he spent the night in the Sheraton Hotel, Mehun said.
"We have received no request for information about him either from Interpol or the Spanish authorities," the spokesman said.
Mehun said on Wednesday that there was no record of the African politician ever visiting Croatia.
Towards the end of 2004, Moto fled to Spain following a failed coup on President Teodoro Obiang Nguema Mbasogo.
Earlier this week Spanish newspapers reported that Moto had disappeared after visiting Croatia in March. Spanish authorities fear that he has been killed.
Equatorial Guinea had sentenced the opposition leader in absence to 62 years' imprisonment for involvement in the attempted coup.
This sub-Saharan country, Africa's third largest oil producer, has been under Obiang's rule since 1979 when he seized power in a coup.