Senior ministry officials were all present at the annual rod nam dam hua ceremony ahead of the Songkran festival, except for permanent secretary Kittipong and two other officials.
Mr Kittipong was criticised by caretaker Justice Minister Chaikasem Nitisiri, caretaker Deputy Prime Minister Surapong Tovichakchaikul and the Centre for the Administration of Peace and Order (Capo) on Wednesday for warmly greeting People's Democratic Reform Committee (PDRC) members when they "visited" the ministry on Tuesday and sitting down for talks with anti-government leader Suthep Thaugsuban.
The Suthep meeting led to Capo's ordering a ban on all top state officials showing any support for the anti-government movement during working hours.
Permanent secretaries of all ministries have been ordered to a meeting with Capo chiefs next Thursday, when the law will be laid down.
Mr Chaikasem explained he had to criticise the permanent secretary as the meeting with Mr Suthep was inappropriate, but denied any conflict with him. He stressed the need for all ministry officials to remain neutral.
The minister said he understood Mr Kittipong's decision not to show up at the ministry for the celebration.,
Mr Kittipong called in sick on Thursday before the ceremony began, a ministry source said.
Ministry inspector Khunying Pornthip Rojanasunan and deputy permanent secretary Pol Dusadee Arayawut were also absent. It was not known why.
Mr Kittipong has strongly supported reform before a new general election, but has distanced himself from being seen as a PDRC supporter.