Interpol said no checks of its database had been made by any country on an Austrian and an Italian passport between the time that they were stolen and the departure of the flight.
"Whilst it is too soon to speculate about any connection between these stolen passports and the missing plane, it is clearly of great concern that any passenger was able to board an international flight using a stolen passport listed in Interpol's databases," Interpol Secretary General Ronald Noble said in a statement.
The police agency said it was in contact with its offices in the countries involved to try to establish the true identities of the passengers who boarded the flight with the stolen documents.
It said it is also checking all other passports on the flight "which may have been reported stolen".
Noble expressed frustration that few of Interpol's 190 member countries "systematically" search the database to determine whether documents being used to board a plane are registered as lost or stolen.
"This is a situation we had hoped never to see. For years Interpol has asked why should countries wait for a tragedy to put prudent security measures in place at borders and boarding gates," he said.
The flight from Kuala Lumpur to Beijing disappeared from radar screens after take-off early on Saturday with 239 people on board, and the craft has not yet been located despite dozens of vessels searching the sea under its flight path.