Connie Hedegaard will be replaced by the Danish Prime Minister Lars Lokke Rasmussen, as head of the historic talks.
Speaking at the 194-nation meeting, Hedegaard said, "With so many heads of state and government having arrived it's appropriate that the prime minister of Denmark presides.
She further said, "However, the prime minister has appointed me as his special representative and I will thus continue to negotiate the...outcome with my colleagues."
Hedegaard, a conservative, was appointed climate minister in 2004.
She was first elected to Denmark's parliament in 1984 and was at the time the country's youngest MP.