Investigators had not uncovered the source of the hack, police spokesman Simon Drobik said.
"We can confirm that the website disruption is due to a cyberattack," he said. The site was not "connected to any critical services" and IT personnel are working on the problem, Drobik said.
The demonstrators, meanwhile, arrived at Civic Plaza holding signs protesting recent police shootings, and activists called on various city officials to resign. They marched about 2 miles toward the University of New Mexico.
Albuquerque police have been involved in 37 shootings, 23 of them fatal since 2010. Critics say that's far too many for a department serving a city of about 555,000.
The U.S. Justice Department has been investigating the department for more than a year, looking into complaints of civil rights violations and allegations of excessive use of force.
Last week, Albuquerque police fatally shot a man at a public housing complex. Authorities said he shot at officers before they returned fire.
In the shooting on March 16 that led to the YouTube posting Tuesday, a homeless man was killed in the foothills of the Sandia Mountains on the east side of Albuquerque. The shooting was captured on video and followed a long standoff.
Anonymous, a loosely organized worldwide hacking group, has been blamed for breaking into confidential information and defacing websites.
The FBI has opened an investigation into the shooting.