Named in the warrants were Chayanin Khonglang, Kongkiat Choothong, Sompat Kwanthong, Sammit Juiplod, Prapas Phakdi, and Wanida Kaewmanee, police spokesman Piya Uthayo said.
The six face charges in connection with the farmers' road and rail blockade and putting public safety at risk, he said.
The move came after rubber farmers blocked the railway between Ban Toon station and Cha-uat station in Cha-uat district to demand the government tackle tumbling rubber prices.
The farmers had earlier set up a blockade on Highway No.41 near Khuan Nong Hong intersection in the district.
Pol Maj Gen Piya Uthayo said Tuesday the police had no policy to use force against the farmers and so far no special law was needed to handle the protest.
His assurance came amid concerns over the possible use of riot police to break up the protest. About 1,100 riot police were Tuesday sent from Muang district to the office of Bo Lo wildlife sanctuary, 20km from the protest base.
The police spokesman said the protest has been joined by other groups with political interests and violence-prone teen-agers, making talks impossible.
However, attempts to negotiate with the protesters continue via local leaders such as kamnan and village chiefs.
Preparations are under way to handle mass rallies by rubber farmers across the country on Sept 3.
The rail blockade Tuesday forced the State Railway of Thailand to suspend five South-bound train routes. However, train services from Phatthalung station southward are unaffected.
A group of kamnan and village heads Tuesday urged the protesters to remove the rail blockade and gather at Khuan Nong Hong intersection.
Led by Pensri Thongboonchu, president of Cha-uat's village head and tambon chief club, the local leaders also called on the protesters to disperse.
A leaflet also circulated Tuesday in the district.
Signed by the people of Cha-uat district, it said the protesters were not locals and they would be thrown out by residents if they refused to leave.
Democrat MP for Surat Thani Suthep Thaugsuban Tuesday denied an allegation he was the politician with the initial "S" who was behind the protest.
He said the accusation was baseless and the protest was the result of two years of government negligence in addressing low rubber prices.
Mr Suthep called on Prime Minister Yingluck Shinawatra to address the rubber price problem and respect the farmers' right to demonstrate the way she did with red-shirt protesters.
He said Ms Yingluck should assign her deputy to hold talks with protesting farmers and rubber traders instead of sending Suporn Atthawong,who is a PM's deputy secretary-general.
Nipit Intarasombat, Democrat MP for Phatthalung, hinted there had been attempts to "buy out" some protest leaders.
Pheu Thai spokesman Prompong Nopparit denied the government was applying double standards.
He said the government sent a representative to talk to the farmers and it was agreed raw sheet rubber would be bought at 80 baht/kg.
He said the remaining protesters were from other areas and could have been sent there by certain politicians.
In parliament, Ms Yingluck Tuesday appeared briefly during a joint sitting of parliament debating charter amendment and she was pressured to address the issue of falling rubber prices.
Democrat list-MP Jurit Laksanavisit demanded Ms Yingluck give assurances the government would not use force to break up the rubber farmers' protest.
He said the farmers would be happy if the government guaranteed the rubber price at 100 baht/kg.
Ms Yingluck agreed to look into the issue and ask the relevant authorities to deal with the problem.
Mr Jurit, however, carried on prodding her about rubber prices, prompting Pheu Thai MPs to protest that the issue should be left for discussion Thursday.
Pheu Thai MP for Chiang Mai Jullapat Amornwiwat suggested Mr Jurit talk to the prime minister personally so Mr Jurit walked up to the prime minister and talked to her for a minute.
Ms Yingluck left the meeting after the one-minute encounter.