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.

Marcos Rojo put Argentina ahead from Lionel Messi's free-kick and Javier Pastore made it 2-0 with a low shot.
Lucas Barrios pulled one back from 20 yards, but Angel Di Maria then netted twice, slotting in from Pastore's pass and then converting a rebound.
Sergio Aguero headed in a fifth and Gonzalo Higuain blasted in a sixth.
It was an impressive victory from Gerardo Martino's side as La Albiceleste moved into the Copa America final for the third time in four competitions and will play Chile in Santiago on 4 July.
Although he did not score, it was another influential performance from skipper Messi, who had a hand in three of the six goals.
His free-kick led to Rojo opening the scoring in the 15th minute and then the four-time World Player of the Year created the second with a jinking run before setting up the impressive Pastore.
Paraguay, 85th in the world rankings, had recovered from a two-goal deficit in their group game against Argentina, which ended 2-2.
Barrios, who scored a last-minute equaliser in that match, netted again, just before half-time with a fine effort from 20 yards out.
But there was to be no fightback this time. Early in the second half, Pastore released Di Maria who slid the ball underneath goalkeeper Justo Villar.
Argentina made it four as Messi led a counter attack and set up Pastore, whose shot fell to Di Maria to finish into an open goal.
Di Maria's cross was then headed in by Manchester City striker Aguero before substitute Higuain scored a stunning sixth to complete the rout.

Atherton, 28, has won all seven races this season and 13 in a row, a run stretching back to 2015.
The world champion had already sealed the 2016 World Cup crown in Canada last month but won in Andorra on Saturday to end the World Cup season unbeaten.
She has now won five overall World Cup titles in downhill.
Wales' Manon Carpenter completed a British one-two in the overall standings, finishing 560 points behind Atherton.
Trek Factory Racing's Atherton won the final race by 6.5 seconds ahead of Australian Tracey Hannah and Myriam Nicole of France.
In the men's event, Britain's Danny Hart won his third consecutive World Cup race but finished second in the overall standings behind American Aaron Gwin.
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.
[NEXT_CONCEPT]
Argentina remain on course to win their first Copa America title since 1993 after thrashing Paraguay to set up a final against tournament hosts Chile.
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Britain's Rachel Atherton completed the first "perfect season" in UCI Downhill Mountain Bike World Cup history with victory in the season's final race.