"We will try to organise better the facilities until the end of November... in order to start the process of relocation," Tsipras told reporters.
"We have to organise the hotspots (for) the procedures of registration and identification of refugees," he said.
Under an agreement with the European Union, Greece will expand its so-called "hotspot" registration centres on the Aegean islands where over 400,000 people have arrived since the beginning of the year, most fleeing the civil war in Syria.
Tsipras also said Athens should step up cooperation with neighbouring Turkey to protect refugees, hundreds of whom have died trying to cross the Aegean.
"We have to cooperate with the Turkish authorities... to organise better conditions (so) the refugees (will) not take the risk to lose their lives in the Aegean sea," he said.
Also on Tuesday, the EU border agency said a further 600 officers would be sent to Greece to assist with border control and registration duties. A hundred of them would be from Austria, Faymann told Tsipras.
The Austrian chancellor said the EU should consider building camps near Syria to keep refugees closer to home. He said it should be a "priority to finance camps in the region of Syria, so that people have the possibility to have their human rights within the region".
Many of them would be happy to stay in the region if they were able to live in peace, he said.