The minister was speaking in the backdrop of a country-wide signature campaign against the government decision launched by wives of Army officers.
At a press conference, Ms Sitharaman said a total of 850 roads were closed in various cantonments, out of which 119 were blocked without following laid down procedures and now some of them have been opened.
The Defence Ministry last month had decided to allow civilian access to the roads in 62 cantonments after Ms Sitharaman held a meeting on May 4 with a group of MPs, elected office-bearers of cantonment boards and Army officials.
A large section of Army officials and their families have expressed strong reservations over the decision to reopen all roads in cantonments to civilians, citing security concerns. Veterans and wives of armed forces personnel have been agitating on the issue.
"I met the wives of the Armed Forces personnel and heard their concerns which were largely about the security. I fully appreciate that," she said.
Ms Sitharaman said the defence ministry held a series of meetings with all stakeholders including the Army before deciding to open up the roads for civilians.
The defence minister said that before the May 4 meeting with elected representatives, she held four meetings with senior Army officials.
"The order by the ministry of defence addresses traffic related issues. Places where unit lines exist or where families of our servicemen are living, we are cautious about its security," said Ms Sitharaman.
She said, "If you (army) decide to close the roads based on intelligence input, you are welcome to do so. But follow due procedure."
A country-wide signature campaign against the government decision has been launched by wives of Army officers. They say they would meet the defence minister urging her to reverse the cantonment board decision.
The MPs and elected officials of cantonment boards had strongly pitched to allow civilians unhindered access to the roads.
The ministry had said that it was decided that a simplified detailed standard operating procedure will soon be issued to address the needs of the local public and the military establishment.
However, families of Army officers feel the decision may expose the cantonments to security risks as military bases have recently been targeted by terrorists in Jammu and Kashmir and other areas.