The U-turn came less than 24 hours after the airline announced that passengers cannot check-in baggage for Tuesday and Wednesday flights to the two European cities due to "unseasonably strong headwinds" on a longer flight path it is taking.
The airline said it recently had to operate a longer route to Europe, via Egyptian airspace, for safety reasons. It said strong headwinds over the past four days were in excess of 200 knots, which can add up to 15 percent to fuel burn on its Boeing 777 aircraft.
It didn't elaborate on the change in route, and airline officials could not be reached immediately for comment. A Malaysia Airlines jet flying from Amsterdam to Kuala Lumpur was shot down by a missile in eastern Ukraine in 2014, killing all 298 people on board.
Losses of two flights in 2014 hit the finances of already struggling Malaysia Airlines. One flight heading to Beijing disappeared and is believed to have crashed in the Indian Ocean. That tragedy was followed months later by the Ukraine disaster.
Last year, the airline appointed its first foreign CEO, Christoph Mueller, the former head of Ireland's Aer Lingus, to oversee a major restructuring. Mueller has said the airline can break even by 2018 after cutting 6,000 staff, selling surplus aircraft and refurbishing its international fleet.