The 28-year-old woman officer, posted in a state government department, had recently accused the senior civil servant of sexually harassing her "for writing adverse comments on official files".
"While the woman officer appeared before the commission earlier, the senior IAS officer recorded his statement today," Haryana Women's Commission Chairperson Pratibha Suman said.
She said the complainant reiterated her allegations, and the senior official rubbished the charges against him.
"The entire matter is subject to further investigations. However, at the preliminary stage it appears that the matter may just be a case of harassment," she said.
Ms Suman said both the officers have pledged full cooperation during the investigation.
"Today, while we were recording the senior IAS officer's version, we also called a director-level officer from his department. If needed, we will also question 3-4 officers from the department," she said.
The senior IAS officer had earlier rubbished the allegations and claimed that the woman officer had been advised "not to find faults with the files which have got all necessary clearances from other officials".
She had written that the male officer, her boss, summoned her to his office on May 22 and "threatened" her.
"He questioned me why I write on files the wrongs the department has done," her post read.
The superior's officer allegedly threatened to file a complaint and "spoil her Annual Confidential Report (ACR) if she did not stop writing adverse comments on the official files".
The senior IAS had, however, said that the allegations levelled against him were "false and baseless".
He had also said that the woman officer had been "finding faults" with every official file and he had advised her that it was not appropriate for her to do so on the files which have the necessary clearances from others.