Rehn said: "Failure to meet legal obligations cannot remain without consequences."
Tony Blair, the British prime minister, warned that it would be a "serious mistake" to send a negative signal to Turkey over its EU membership bid.
"It means you suspend nearly the whole process. It's too much"
Caglar Cakiralp, permanent delegation of Turkey to the EU
Angela Merkel, the German chancellor, who is due to take on the EU's rotating presidency for six months in Janurary, called for better checks on Turkey's progress in EU membership.
She said: "The Commission proposal is a strong signal that the Ankara protocol has to be accepted by Turkey.
"A stronger verification clause would be desirable so that the council can review Turkey's progress, perhaps in 18 months' time."
José Luis Rodriguez Zapatero, the Spanish prime minister, and Anders Fogh Rasmussen, the Danish prime minster, also voiced support for a partial suspension in talks.
Caglar Cakiralp, the first secretary of the permanent delegation of Turkey to the EU, said: "It means you suspend nearly the whole process. It's too much."
EU members will make a final decision on the proposal during their summit on December 14-15.
For months the EU has been threatening full or partial suspension of membership talks with Turkey over the ports issue.
Ankara refuses to act until the 25-nation bloc keeps its 2004 promise to ease economic sanctions imposed on the island's breakaway Turkish Republic of Northern Cyprus (TRNC), recognised only by Ankara.
Finland, a supporter of Turkey's EU membership, has been trying to resolve the stalemate since September with a proposal that included Turkey opening its ports and the EU trading directly with the self-proclaimed TRNC.
But Helsinki said on Monday there was no hope of an agreement during its EU presidency, which concludes on December 31.
Christof Ides, Cyprus' spokesman for its representation to the EU, argued that freezing a few chapters temporarily would have no effect on the membership process as other chapters would be opened instead.
"Nobody wants to see the European summit sidetracked by Turkey"
However, he added that any accession chapters that were opened with Turkey would not be formally closed until the EU was satisfied that Turkey was complying with its obligations.
"The decisions will be taken after a fully-fledged discussion in the council [of member states]."
EU negotiations with Turkey began in October 2005.
Turkey's accession process is already expected to take at least a decade and no guarantees have been given of it eventual success.