The father of four young children was arrested in the middle of the night at his home just a short drive from Dubai International airport.
"Amnesty International is appalled and dismayed at this surprise overnight raid resulting in the arrest of Ahmed Mansoor, a courageous and prominent human rights defender in the United Arab Emirates," said Lynn Maalouf, Director of Research at Amnesty International's Beirut regional office.
Amnesty said it believed Mr Mansoor was detained for the peaceful expression of his beliefs.
It said security officials "stormed" the family's apartment and carried out a lengthy room-by-room search, including of the children's bedroom.
It said authorities did not inform Mr Mansoor's wife where he was being taken.
Mr Mansoor was one of the last human rights defenders living in the UAE.
Dozens of activists and writers have been jailed in recent years for speaking out against the royal family that rules the country.
The NGO is calling for Mr Mansoor's immediate release.
The wealthy Middle East country has close military ties to the Australian Federal Government.
Yesterday Australian ambassador to the UAE Arthur Spyrou tweeted that he was "excited" to co-host an event with the UAE at the UN marking the International Day Of Happiness.
In 2015, Australian woman Jodi Magi was jailed and then deported for writing a post on Facebook that an Emirati couple complained about.