"A final SMS text message from him to his colleagues, sent at 10:00am local time, said that he was being removed from the airplane and was asking for help," HRW said in a statement.
His current whereabouts are unknown, HRW said.
"Turkmenistan has a long history of torturing and mistreating detainees in custody," it said.
"Zatoka should be released immediately, and before that happens the Turkmen authorities should reveal where he is and allow him access to an attorney."
His detention comes three months after Ogulsapar Muradova, a local reporter of Radio Free Europe/Radio Liberty, died in jail after her arrest on charges of illegal weapons possession.
Environmental sources in Turkmenistan confirmed Zatoka's detention but could not give further details.
Amnesty International said in a separate statement that Zatoka, who is a citizen of Russia and of Turkmenistan, was "at great risk of torture or other ill-treatment".
Zatoka, who had been due to fly to Moscow to meet ecologists and his family, helped set up an environmental group in 1992 shut down by a Turkmen court in 2003. Zatoka has worked as an independent ecology specialist since then, HRW said.
Amnesty said it was concerned about a continuing clampdown which has "led to many civil society activists, political dissidents, members of religious minority groups and their families being arbitrarily detained, tortured or ill-treated and imprisoned after unfair trials".