The Portland Press-Herald reported "Long live the West" and "Free Cyprus" was also spray-painted on the mosque.
Portland has a relatively sizable Muslim population thanks in part to a large population of immigrants from Somalia and Sudan, Police Chief James Craig told TPM in an interview. The city of about 66,000 has three mosques.
Hate crimes are uncommon in the Portland, Craig said, and crimes targeting Muslims almost unheard of.
"This is the first [hate crime] targeting religion," in 2011, he said.
The department has no leads so far in the case of the mosque vandalism, which has already been painted over. Craig said he's reached out to the FBI and informed the agency of the incident though whether federal agents will get involved is unclear. The FBI did not immediately respond to a request for comment.
The hate crime designation means that if and when someone is caught, they would face what Craig called "an enhancement" on what would likely be vandalism charges.
Craig was due to meet with Muslim leaders later in the day, and said that the hate crime was a shock in a city known for being "outwardly supportive" to its immigrant population.
"This is not reflective of the Portland community," he said. "Absolutely not. In fact, this is an anomaly."
Members of the mosque told local press in Portland that the vandalism was jarring.
"It makes me feel like I'm not welcome," mosque Treasurer Abdiaziz Mohamed told the Press-Herald.