The 75-member parliament voted 41 to 34 in favour of a secret vote for a no-confidence motion brought by the main opposition, Maldivian Democratic Party (MDP).
Analysts said the decision to have a secret ballot was a blow to Waheed's government which has been in office since the MDP President Nasheed was ousted on February 7 this year.
The MDP has submitted a resolution calling for the removal of Waheed and claim confidence of obtaining the required numbers.
The Speaker of Majlis will fix the date for the motion to be taken up.