A breakdown in communication led to a spill that dumped more than 500,000 gallons of sewage into the ocean at Ala Moana Beach Park on Monday morning, a city official said Tuesday.

“It never should have happened,” city Environmental Services Director Lori Kahikina said. “We knew the storm was coming.”

A key pump station that should have been up and running during the storm was inoperable because the contractor in a major construction project at the Keawe Street pump station left the facility offline, Kahikina said.

Without the station operational, the sewer system was overwhelmed during heavy rain Monday morning. The back-flow ended up escaping through manholes at the intersection of Atkinson Drive and Ala Moana Boulevard, entering the ocean through storm drains.

Honolulu experienced more than 3 inches of heavy rain Monday, far exceeding the previous record for that day in 1966.

The city is expected to reopen Ala Moana Beach Park on Wednesday morning but will keep the ocean off-limits until water samples show improvement in contaminant levels.

Officials said the earliest the beaches would reopen would be Wednesday afternoon.

City workers sanitized the portion of the park affected by the spill Monday night and Tuesday morning.

Appearing to be rattled by a shot of negative nationwide publicity, officials emphasized that while Ala Moana Beach was closed due to the spill, the Waikiki beaches were shut down primarily because of the brown-water advisory that was issued by the state Department of Health for the entire state because of storm runoff.

City spokesman Jesse Broder Van Dyke said the Waikiki beaches were closed “out of an abundance of caution.”

The Honolulu Zoo was also overwhelmed with stormwater that wound up flowing into the ocean Monday, and there were reports of feces in the water near the Kapahulu Groin.

“This is a still very serious matter,” said Shayne Enright of the city Emergency Services Department. “Lifeguards are continuing to urge people not to go into the waters because of the health risk.”

Department of Health workers Monday and Tuesday took water samples for testing from 20 shoreline areas — from Kakaako Waterfront Park to the end of Waikiki.

Kahikina said the miscommunication problem that led to the spill would be the subject of a meeting set for Wednesday between the Environmental Services Department and the city Department of Design and Construction.

The pump station that wasn’t working was part of a larger $175 million construction project designed to improve capacity and prevent sewage spills, a requirement under a 2010 Environmental Protection Agency consent decree.

Design and Construction was overseeing the project, while Environmental Services operates the pump station.

The decree required the city to put two additional force main pressurized sewer pipes under Honolulu Harbor to the Sand Island Waste Treatment facility, the first phase of a project that was completed in the last few months.

The second phase was to connect the pipes to a T-valve at Ala Moana No. 2 Pump Station on Keawe Street, Kahikina said. The problem was that the other end of the T-valve needed a steel plate, and that wasn’t connected and sealed, leaving the station inoperable during Monday’s deluge.

“That is purely our fault,” Kahikina said. “Between my department and Department of Design and Construction, we definitely should have improved our communications so that the (steel plate) was put on. Because with that (steel plate), the spill would not have happened.”

Kahikina said the pump station could have been down for months, but, she added, it wasn’t the contractor’s fault.

“We knew a storm was coming, and my operator should have communicated to the Department of Design and Construction and said, ‘Hey, I needed the pump station running because I can’t handle all the excessive rainwater coming in.’”

The station, designed to handle 100,000 gallons of sewage a day, was finally connected only after Monday’s storm, officials said, and is now running in case there is more heavy rain this week.

Kahikina said city officials have discussed the possibility of merging the two departments, in part, to help improve communication.

Keith Kawaoka, state Department of Health deputy director of environmental health, said his department would be conducting an investigation into the spill to determine whether there are any violations of the U.S. Clean Water Act. The state department is the local agency with authority to enforce the federal law.

In 2010 the city agreed to make more than $3.5 billion in improvements to its sewage treatment system and pay a $1.6 million fine. The consent decree was with EPA, the state Department of Health and three environmental groups that sued the city.

The fine was intended to resolve violations of federal and state law for past sewage spills, including the sewer main break that resulted in the discharge of about 50 million gallons of sewage into the Ala Wai Canal in 2006.

As a result of the consent decree, the city promised to upgrade its wastewater collection system and treatment plants over the next 25 years.