An EU-Canada trade agreement will include controversial investor protection clauses, the EU's new trade commissioner has confirmed.

Following a meeting in Berlin on Monday (10 November) with Sigmar Gabriel, leader of the SPD and a minister in Angela Merkel's coalition government, Cecilia Malmstrom said that only "minor clarifications and adjustments" could be made to the EU-Canada deal, known as CETA.

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Trade officials have so far spent more than four years negotiating the draft text.

The investor protection clauses, known as investor state dispute settlement, have become the most controversial part of both CETA and the talks on a transatlantic trade and investment partnership, known as TTIP, with the US.

The centre-left Socialist and Democrat group, to which Gabriel's SPD belongs, is conditioning its support for TTIP and CETA on the removal of investor protection clauses which, it says, could make it easier for companies to sue governments if legislation adversely affects their investments.

"The chapter regarding investment protection is not approvable," Gabriel told deputies during a debate in the Bundestag in September.

However, despite telling MEPs at her parliament hearing last month that excluding ISDS from the EU-Canada deal could "unravel the agreement", Malmstrom has left her options open on whether to include the clauses in TTIP.

Having been formally signed off by EU and Canadian leaders in September, CETA will be put in front of MEPs in 2015, needing a parliamentary majority if it is to be successfully ratified.

Meanwhile, with the Greens and left-wing Gue group vocally opposed to the trade deals, both TTIP and CETA face an uncertain ratification process.

Campaign groups demanding that the Commission halt its work in negotiating free trade deals have also upped their activities in recent months.

On Monday the Stop TTIP coalition, composed of over 300 campaign groups from across Europe, filed a lawsuit against the European Commission to the European Court of Justice in Luxembourg in protest at the Commission's refusal to accept their citizens' initiative aimed at halting the trade talks.

In September the Commission refused to accept an anti-TTIP petition which campaign groups had wanted to be classified as a European Citizens' Initiative (ECI).

Under the Lisbon treaty, a petition must be signed by more than one million Europeans and relate to a piece of EU policy-making to be classified as an ECI.

The EU executive ruled that the petition was inadmissible as a citizens' initiative because it did not relate to law or policy that is already in force.

Had the initiative been accepted it would have required the Commission to review its policy on the trade talks and to hold a public hearing in the European parliament.

Michael Efler, a member of the campaign group behind the initiative, said that the Commission's position "effectively prevents any future ECIs on international agreements“.

"When it comes to the negotiation of international treaties, the European Commission wants to exclude citizens. While they are being negotiated, people are told not to interfere and when final contracts are put on the table, it’s too late," he added.

A second anti-TTIP petition launched last month has now gathered more than 850,000 signatures.