However, a review of physical and historical evidence showed Van Gogh painted them, probably in the spring of 1886 while he was studying under the painter Fernand Cormon in Paris.
Chemical analysis showed the paint was identical to other works definitely attributed to Van Gogh in that period.
On the back of one of the portraits was the stamp of a paint merchant near where Van Gogh lived with his brother Theo at that time, the museum said in a statement.
The picture frames also were by the same manufacturer as other confirmed Van Goghs of that period, Bos said.
A thorough review of Van Gogh's work turned up other pieces that were stylistically similar.
"The combined weight of all this evidence offers convincing grounds for the reattribution of these two female portraits to Van Gogh," the museum said. The identity of the women "remains a mystery."
Although Van Gogh is now seen as one of history's greatest painters, few recognized his talent during his lifetime, and he was increasingly troubled by mental illness.
He died of a self-inflicted gunshot wound in 1890 when he was 37.