The court issued the warrants late in the afternoon after protest leaders told the red shirts camped out at Government House to go home before turning themselves in around noon.
The warrant said Thaksin was sought for inciting unrest that led Prime Minister Abhisit Vejjajiva to cancel the Asean summit in Pattaya and impose a state of emergency that led to military crackdowns on protesters.
"Thaksin and his allies are charged by court for illegal assemblies of more than five people, threatening violence and breach of peace, punishable by five years in jail," the warrant said.
It said the former PM was also accused of inciting people to break the law and cause unrest, a charge punishable by seven years in prison.
Red-shirt protest leaders, Veera Musigapong, Natthawut Saikua and Dr Weng Tochirakarn turned themselves in at the Metropolitan Police Bureau headquarters.
Before surrendering, Weng told the red shirts that they had to move out of Government House not because they had lost but because they had to change their stronghold and rally strategies. He said basing themselves at Government House would put them at a great disadvantage, adding that he would take legal action against Abhisit for killing citizens.
Natthawut told the red shirts that the rally had to be called off temporarily because they did not want more losses of lives.
As their leaders were telling them to disperse, the red-clad protesters objected saying they wanted to continue fighting in Sanam Luang. However, upon refusal, they got upset and some even broke into tears.
Protest leader Jakrapob Penkair, who disappeared while others were surrendering to police, told reporters on the telephone later that he would definitely not turn himself in, adding that the red shirts would continue protesting, but their strategies would be discussed later.
He also said that though he did not know the whereabouts of Pheu Thai Party MP and fellow protest leader Jatuporn Prompan, he knew that he was safe.
After being interrogated by police, the three protest leaders held a press conference. Natthawut said he was against moves to have him and his counterparts detained at a different unit or a military camp because their charges were for wrongdoings they had allegedly committed before the state of emergency was imposed.
Later their lawyers said police agreed to detain them at the Metropolitan Police Bureau Headquarters until they were granted bail.
Apart from Thaksin, the 13 people wanted are Veera, Jatuporn, Natthawut, Jakrapob, Weng, Adisorn Piangket, Sirawit Pimklang, Peera Pringklang, Narongsak Mani, Nattapong Intanang, Shinawatra Habunpad, Arisman Pongruangrong and a man only identified by his photo.
Police yesterday issued arrest warrants for five men suspected of leading red-shirt protesters for wreaking havoc in Pattaya on Saturday. The five are Siriwan Nimitsilapa, Tornchai Sakmangkorn, Surachai Danwattananusorn, Sakda Noppasit and Pol Lt-Colonel Waipot Apornrat.
Yuthana Cherngproey, a representative of the Asean meeting venue, Royal Cliff Beach Resort, filed a complaint with police estimating damages to the hotel at Bt141,824.
Arisman, who was detained on charges of inciting unrest in Pattaya, won temporary release yesterday.
The Pattaya Provincial Court approved his request for bail despite objections from the police on grounds that protesters in Bangkok had been dispersed.