Lt Gen Chatudom Titthasiri, the committee's spokesman, said the panel vetting the bill concluded that policies set by Office of the Public Sector Development Commission to award bonuses were insufficient and non-standard, as bonus payments differed every year.
The five billion baht was shifted to the Central Fund instead, he said.
The committee instructed the OPDC to review its bonus-payment policies and propose new criteria for consideration. If the government approves them, the five-billion baht would be restored, Lt Gen Chatudom said.
Asked about fallout from angry civil servants, Lt Gen Chatudom admitted the issue was sensitive and may affect morale. But he insisted the OPDC criteria was too murky.
However, he noted, a cut in bonuses could be offset by increases in base pay offered up by NCPO chief Prayuth Chan-ocha. The OPDC is still studying the wage increases proposed for next year.
The National Legislative Assembly will debate the 2015 budget during its second and third readings Sept 17.