The military denied shadowing former prime minister Yingluck Shinawatra to prevent her fleeing the country to avoid criminal charges in the Supreme Court.
The denial came after troops and police stopped her motorcade at a checkpoint in Chiang Mai Tuesday.
The army says the checkpoint was for the former premier's protection, but after public criticism officials later agreed to dismantle it.
Deputy Prime Minister Prawit Wongsuwon, who oversees national security, said the measure was carried out at the discretion of local soldiers and police, and was not ordered by the National Council for Peace and Order.
Ms Yingluck travelled to Chiang Mai on Monday to attend a merit-making ceremony for her ancestors at Wat Rongthamsamakkhi in San Kamphaeng district.
Soldiers and police searched Ms Yingluck's motorcade at a checkpoint set up Tuesday at the entrance to the Green Valley Housing Estate in Mae Rim, where her Chiang Mai home is located.
Ms Yingluck and her entourage were heading to Wat Romgthamsamakkhi for the merit-making ceremony when they were stopped.
Gen Prawit said it is normal practice for the authorities to provide security for VIPs. "Officials do not fear she will flee [the court case]. She is a former prime minister. Authorities only wanted to show good intentions towards her," he said.
Ms Yingluck is charged with dereliction of duty for failing to stop losses and corruption in her government's rice-pledging programme, in violation of Section 157 of the Criminal Code and the National Anti-Corruption Act.
The Office of the Attorney-General (OAG) is preparing to indict her in the Supreme Court's Criminal Division for Political Office-Holders.
The commander of the 33rd Army Circle, Maj Gen Sarayuth Rangsri, also denied the checkpoint was part of efforts to monitor Ms Yingluck's movements to stop her from fleeing.
He also called it a courtesy offered to a VIP.
"We apologise if our actions upset the former prime minister. But soldiers and police set up the checkpoint as a security measure because she had arrived. We had no intention of intimidating her," Maj Gen Sarayuth said.
Maj Gen Sarayuth said officers did not search Ms Yingluck's vehicle, but admitted other cars in the motorcade were searched.
The inspections were conducted legally, Maj Gen Sarayuth said, adding the former prime minister was treated with respect.
Maj Gen Sarayuth said the checkpoint would be removed, but soldiers and police will provide security for Ms Yingluck during her stay in Chiang Mai.
Ms Yingluck's trip to Chiang Mai follows a National Council for Peace and Order ban on her travelling abroad.
Meanwhile, Ms Yingluck has been told to report to the OAG on Feb 19, National Anti-Corruption Commission chairman Parnthep Klanarongran said Tuesday. From there, she will be taken to the Supreme Court to be formally indicted on the rice scheme charges, Mr Parnthep said.