New security checks at Brussels Airport, where Islamic State suicide bombers killed 16 people in March, are creating huge queues and causing passengers to miss flights, a situation the airport operator described as "bizarre".

Belgium's main airport reopened part of its departure hall on Monday, bringing capacity up to about 80 percent from 20 percent when operations initially restarted a month ago, after the attack on March 22 gutted parts of the building.

But passengers complain police checks at the entrance to the building are causing delays of several hours and have created a new security risk by forcing people to congregate outside.

"You couldn't find a better target," said a senior Belgian security official who is not involved in the airport plan.

Former Belgian prime minister Yves Leterme missed his flight to Budapest after queuing for two hours and 40 minutes.

"In the coming weeks I'll think twice about choosing Brussels Airport," Leterme told Belgian daily Het Laatste Nieuws. "I think Paris is the better option."

With major airports in Paris, Amsterdam and Duesseldorf easily accessible by train from Brussels, the chaos in the Belgian hub could have a major economic impact.

The manager of the airport, which also suffered disruption last month due to industrial action by air traffic controllers, blamed police unions for taking the decision to screen every passenger and their luggage at the entrance.

"We worked day and night for 40 days to reopen the airport and some police union representatives hold onto that bizarre system of pre-check-ins," president of the board of Brussels Airport Marc Descheemaecker wrote on Facebook.

"Abandon it... We are shooting ourselves in the foot and making fools of ourselves abroad."

Police union VSOA blamed a lack of staff among private security firms which carry out the initial checks.

"We are open to suggestions about how to improve the checks but one thing is clear, security at the airport has to be better than before March 22," a VSOA spokesman said.

The Interior Ministry, ultimately responsible for security, said it would hold talks on Tuesday to address the situation.

An official of another police union was quoted by Belga news agency as saying an agreement had been reached to check only some passengers and bags before they enter the check-in area.

Brussels Airlines, partly owned by Lufthansa, saw passenger numbers decrease 20 percent in April due to reduced capacity at the airport where it is the main operator. – Reuters