The police operation to remove the activists began on Tuesday morning after a "number of people were detected" on the bridge about 5.15am.
Police allege the group blockaded security who tried to stop some members abseiling off the bridge to unfurl banners, which allowed six of them to scale the fence.
Climate change had been a key issue during the election campaign in which Labor leader Bill Shorten had criticised the Coalition government for inaction.
Earlier in the operation ten people were arrested.
The group said its supporters had "occupied" the iconic bridge and that six trained climbers had abseiled from it.
They were all conditionally bailed, charged with climbing the bridge and willfully preventing the free passage of a person/vessel.
A number of protesters were detained by the security personnel, though others were able to climb under the structure and abseil under a public walkway.
Police have now confirmed that the remaining three who were suspended from ropes beneath the bridge, have been removed and arrested.
Climate change activists have scaled Sydney Harbour Bridge, with at least three reportedly arrested.
Ten were taken to local police stations for questioning.
Police are at the scene directly above the three protestors.
Greenpeace Australia Pacific chief executive David Ritter hopes the protest will be recognised by the main political parties.
Coal is the biggest cause of climate change: we need 100% renewables, stat.
Morrison said Australia would meet its commitment to the 2015 Paris climate accord but enacting stronger targets would damage its finances.
A group of indigenous Torres Strait islanders lodged a formal complaint against the Australian government at the United Nations on Monday, claiming that their climate inaction violated their basic human rights.