The petition calls on the EU and its member states to stop the talks on the Transatlantic Trade and Investment Partnership or TTIP.
It also says they should not ratify a similar deal that has already been done between the EU and Canada.
It says some aspects pose a threat to democracy and the rule of law.
One of the concerns mentioned in the petition is the idea of tribunals that foreign investors would be able to use in some circumstances to sue governments.
There is a great deal of controversy over exactly what this system, known as Investor State Dispute Settlement, would enable companies to do, but campaigners see it as an opportunity for international business to get compensation for government policy changes that adversely affect them.
This kind of provision exists in many bilateral trade and investment agreements.
Friends of the Earth have published new research on the impact they have had on EU countries.
Information about these cases is not always made public, but the group says that going back to 1994, foreign investors have sought compensation of almost €30bn (£24bn) from 20 states. Where the results are known (a small minority of the total), the tribunals have awarded total compensation of €3.5bn (about £2.8bn).
In Britain, the possible implications of this provision for the National Health Service have been especially controversial.  Campaigners believe that the investor tribunals would make it harder to reverse any decisions to contract services out to international healthcare firms.
John Hilary of War on Want said:  TTIP  "will make it impossible for any future government to repeal the Health & Social Care Act and bring the NHS back into public hands".
The petition lists a number of other areas where its signatories believes European standards would suffer if the TTIP negotiations are completed and the Canada deal is ratified:  employment, social, environmental, privacy and consumer protection.
The European Commission says the EU will not have to sacrifice its high standards. It also says investor protection provisions are important for investment flows and have in general worked well. But it accepts there is a need for improvement and is trying to achieve that in its bilateral negotiations.
The petition has been organised as an exercise called a European Citizens' Initiative which can lead to a public hearing in the European Parliament and require the European Commission to give a formal response explaining why it is accepting or rejecting what the petitioners call for.
The European Commission has already said that the petition doesn't qualify as such an Initiative. Campaigners have launched a legal challenge to this decision.
A campaign group website says over a million people in the European Union have signed a petition against trade negotiations with the United States.