"There remain some important issues to resolve, and obviously nothing is resolved until everything is resolved," Harper said Thursday during a visit to Ottawa by French Prime Minister Jean-Marc Ayrault.
"Obviously, we will only sign a deal when we're convinced we have a deal that is comprehensive and in the best interests of the Canadian economy."
Harper and Ayrault both said an agreement with Canada would be important for the Europeans because it would provide momentum as they embark on separate free-trade talks with the United States.
"It would be an added benefit to us to get this done long before the Americans do such a deal," Harper said.
"For the Europeans, it would be important to get this beachhead to Canada in terms of its own ambitions for a deal with the United States."
Ayrault said a successful Canada-EU pact could have a positive influence on a future deal with the U.S.
"It will not be without influence in terms of the current negotiations taking place between the European Union and the United States," he said.
"We do hope to be the leaders and give the good example with the success of this negotiation. We will be the precursors."
Ayrault said the remaining obstacles to the Canada-EU deal are in the agricultural and intellectual property sectors. Specific hurdles include opening European beef and pork markets and respecting pharmaceutical patents.
"Things are progressing very well," he said. "The most sensitive issues have to do with balanced exchanges in the agricultural sector."
Ayrault and Harper discussed the pact during the French premier's four-city visit to Canada, which began in Ottawa.
Negotiations began almost four years ago. The Harper government was unable to deliver on its pledge to complete an agreement by the end of 2012.
Last month, the European Union's trade commissioner said Canada must change its positions for a deal to be struck, but gave no details.
Karel De Gucht told a committee of the European parliament that he hoped the deal would be sealed soon.
Don Davies, the NDP trade critic, said the government needs to show more accountability and transparency around the continuing negotiations.
"The question for us really is whether or not the Conservatives can competently negotiate a good deal, and defend the important Canadian interests like supply management or our intellectual property regime," he said.
"The Conservatives have adopted an extremely secretive process, and kept Canadians in the dark. We continually have to rely on the Europeans or leaked documents to give us some information about what our government is doing."
Other domestic political hurdles remain for Canada.
Quebec Premier Pauline Marois recently said her Parti Quebecois government could block the agreement if it is deemed unsuitable for her province.
Note to readers: This is a corrected story. An earlier version said information technology was among the remaining obstacles to Canada-EU deal.