Senior veterans will see their monthly stipend cut by more than 20 percent over the next decade, after a smaller initial drop, according to official estimates.
The government says veterans of lower ranks will see less severe cuts to their pensions.
Tsai has said pension reform is her most important task, with official reports warning that an unreformed pension system could be bankrupt by 2020.
But thousands of veterans and other civil servants have regularly gathered outside parliament to protest the cuts.
Dozens of police officers and reporters were injured in a clash in April when protesters threw smoke bombs and used chains to try to pull down a gate and storm parliament.
Tsai said her government has completed the critical reform that "every leader had wanted to do", but did not. "We now have a Taiwan with a sound and well-structured system where every young civil servant, teacher, and military personnel can be sure of their pensions," she told reporters on Thursday. She said the reduced expenditures will be injected back into the pension funds to make them more sustainable.
Tsai admitted some retirement plans will be affected, apologising and thanking veterans for their sacrifice. "It is hard for third parties to understand that feeling of discontent and helplessness for most of those who will have less money in their pockets," she said. But she said the majority can understand the country's predicament "even though there has been a lot of emotions and dissatisfaction in the course of reform". A former lieutenant-colonel will initially see their monthly stipend cut from Tw$70,797 ($2,340) to Tw$69,353, and eventually to Tw$56,360 after ten years, according to government estimates.