Thai and EU officials are gathering in the northern capital this week for the second round of negotiations regarding the free trade deal, which covers a wide range of topics on trade and investment.
The protesters, many of them health activists, demanded the FTA should not include intellectual property rights (IPRs) that go beyond already stringent World Trade Organisation (WTO) obligations.
Any deal beyond the WTO's Agreement on Trade Related Aspects of Intellectual Property Rights (Trips) would only reinforce monopolies by multi-national pharmaceutical companies, increase the price of medicines and create new barriers to accessing cheap generic medicines, they said.
The group also called on negotiators not to include investment provisions that would allow pharmaceutical companies to legally challenge the Thai government in secretive arbitration panels to overrule measures promoting access to medicines.
Act Up-Paris, Oxfam International, Health Action International and Action against Aids Germany said in a joint statement Wednesday they strongly support Thai civil society in their demands.
"EU negotiators should take into consideration the importance of access to cheap and good-quality generic medicines for patients in Thailand when negotiating this trade deal," said Leila Bodeux from Oxfam International.
"Since 2002, a system of universal health coverage has existed in Thailand which covers 99% of the population.
The production and availability of affordable and quality generic medicines is a key element to sustain this universal coverage.
"We fear that should Trips measures or dangerous investment provisions be included in the Thailand-EU FTA, the ability of the Thai government to keep on running the current health system and providing its citizens with the medicines they need might be hampered."
Jacques-chai Chomthongdi, vice chairman of FTA Watch, said it was unlikely the EU would take Thai concerns into consideration. This meant that the Thai delegation must work hard to protect the country's interests by not accepting any demands that would adversely affect Thai health care services, agriculture and the farming industry and benefit-sharing on bio-diversity.
"The EU said it is ready to compromise on these sensitive issues. They agreed to listen to our concerns. But we have yet to see real action," he said.
On Wednesday, 20 representatives of the activist group met EU delegation chief, Joao Aguiar Machado, for about one-and-a-half hours to express their concerns over the deal, particularly the provisions dealing with drug patents, the International Union for the Protection of New Varieties of Plants, and the zero tariff on alcohol products, among others. An EU source said EU negotiators understood the concerns.
A joint statement from Thailand and the EU is expected to be issued Friday.
Buntoon Sethasirote, executive director of Good Governance for Social Development and the Environment Foundation, said the Thai delegates should work closely with the local networks.
"It seems that the head of the Thai delegation has not received well-rounded information," Mr Buntoon said.
"If he takes our concerns as a bargaining tool, it will bring good results.
"The FTA will definitely happen, but I don't know if the results will be poisonous for the Thai people."
Olarn Chaipravat, chief of the Thai delegates, said in a statement the negotiations, particularly on drug patents, will be based on the Trips agreement.
"We have strong concerns about the public's health benefits. The negotiations will not be held outside the Trips framework. The EU itself understands our concerns and insists it will compromise on the issues, based on mutual benefits," he said.