The move followed heated exchanges on social media after it was revealed that MPs were paid more than $3,000 (£1,985) a month.
The average salary in the West African state is about $150 a month.
One MP said the pay cut would promote better governance and rebuild confidence in democracy during a year-long transition to elections.
The former National Assembly in Burkina Faso has been replaced by an interim parliament, the Transitional National Council (CNT), as part of arrangements following the forced resignation of long-serving ruler Blaise Compaore last year.
Mr Compaore seized power in a coup in 1987 and went on to win four disputed elections.
Tens of thousands of people took part in protests in Burkina Faso’s capital, Ouagadougou, in October over moves to allow him to extend his rule, eventually forcing him to step down.
Members of the 90-member CNT have been paid a gross salary plus attendance fees, office allowances, healthcare supplements and fuel costs.
Campaigners, including grassroots political movement Balai Citoyen, have said MPs should not be paid attendance fees and have pointed out the substantial gap between their salaries and average earnings.
Another campaign group, the Coalition Against Costly Life, has said a maximum salary of $900 would be sufficient.
Revelations about MPs’ pay prompted angry reactions on social media, with many saying the pay levels amounted to an abuse of power.
A BBC correspondent in the region, Anais Hotin, says that after fighting for a change of government, people in Burkina Faso are determined to put in place a better system to achieve social justice.
The transitional government is led by Lt-Col Isaac Zida, who was among army officers who took power from Mr Compaore.
He has promised to return Burkina Faso to civilian rule through elections later this year.
Before Lt-Col Zida’s appointment as prime minister, the African Union, the United States and several other countries urged the military to hand back power to civilians or face the prospect of economic sanctions.