The fire in Pedrogao Grande, which ravaged 30,000 hectares (74,000 acres) of forests, was doused only late Wednesday.
The blaze in Gois, the second biggest after Pedrogao Grande, was brought "under control" on Thursday, said Carlos Tavares, the civil protection official leading the operations, though he cautioned that some fires could resume.
Tavares said the fire in Gois had affected 20,000 hectares. The firefighting effort involves nearly 2,400 firemen and water-bombing planes.
Press reports have suggested that Portugal's fire plan had not been revised for four years and that the intense heat might have made some communication antennae malfunction.
The president of the League of Firefighters, Jaime Marta Soares, said Wednesday that he believed arson had caused the fire, contradicting an earlier account by police.
But Marta Soares told local news media the fire had already been burning for two hours before the storm started Saturday.
"I believe, until there is evidence to the contrary... that the fire was of criminal origin," he said.