Regina Lopez said she was disappointed that "business interests" had "manoeuvred the decision".
She had been in the position for 10 months but had not been confirmed.
Congressional confirmations in the Philippines often happen months after ministers start work.
The decision made by the country's Commission on Appointments is final.
Backed by President Rodrigo Duterte, Ms Lopez had ordered 22 out of 41 mines to be closed, and banned open-pit mines.
She also cancelled contracts for undeveloped mines, and said environmental damage was harming the country's poor.
Following the vote, she said: "I'm disappointed because clearly there are business influences that have manoeuvred the decision. And, from my point of view, government should make decisions primarily on the filter of the common good.
"And when business interests take dominant influence in a way that even adversely affects our people, that's not good at all."
The Chamber of Mines of The Philippines said it would seek to undo her measures when a new minister was in post.
"Those have no legal foundation," chamber spokesman Ronald Recidoro said.
"There were no proper consultations held. And more importantly it's really out to kill the mining industry."
Yeb SaÃ±o of Greenpeace Southeast Asia said the sacking "shows how destructive industries continue to hold Philippine lawmakers by their necks."
A spokesman for the president said no replacement had yet been lined up.
Ms Lopez's supporters, who call her an earth warrior, have organised candlelit vigils to mark the end of her tenure.
Lawmakers in the Philippines have removed the environmental secretary, who angered the mining industry by ordering the closure of more than half the country's existing mines.