About a third of lecturers at the University of Papua New Guinea (UPNG) continued their boycott on Wednesday, the interim chancellor says.
Jeffrey Kennedy said contrary to previous reports not all lecturers took part in the boycott which began on Monday.
The number of lecturers not giving classes had declined since then, Mr Kennedy said.
The lecturers are members of the National Academic Staff Association (NASA), who the interim chancellor said was working outside of its mandate.
NASA cited the government's decision to suspend the university council in January as one of the reasons for the boycott.
But Mr Kennedy said NASA's grievances were political and not industrial.
"If they were jumping up and down because of terms and conditions of their members, that's understandable," he said.
"We did check with the office of the industrial registrar and as far as she is concerned there's been no complaint registered with her office.
"In other words, NASA is taking issue on matters that are not industrial related."
Mr Kennedy said whoever was advising the lecturers failed to give them "the full picture" regarding the seriousness of the allegations made against the suspended council.
The new interim council is investigating the allegations and lecturers have been returning to work as they start to understand them, he said.
They include claims of a conflict of interest based on the suspended council's members being mostly UPNG academics.
"So you had a situation where the employees were the employers making decisions on themselves, " Mr Kennedy said.
As a result, systemic corruption was allegedly allowed to occur, including of the UPNG Home Ownership Scheme.
According to the interim chancellor's latest circular, senior staff may have abused the scheme, which gives homes to academics and managers.
"The Interim Council has been advised that Senior Academic Staffs and Senior Management staffs own more then one house and still reside in staff accommodation whilst renting out houses that have been transferred to their names. This is a clear case of Fraud and Double Dipping," the circular said.
Mr Kennedy said the interim council was also investigating claims that sexual favours were exchanged for jobs.
"There are two women that have come forward... The persons accused, they've already been given notice and the suspension letters will be served today."
Bribes or sexual favours for better grades may have also taken place, and the interim council had established a complaints office for students, Mr Kennedy said.
Lawyers had been engaged to devise a "whistle blower protection policy" for students reporting such abuse, he added.
Of the order granted by the National Court to stop the boycott, the interim chancellor said it did not prevent industrial action but restrained the "withdrawal of service without cause".
Mr Kennedy would not comment on whether the interim council would seek to have boycotting staff held in contempt of court but added the court registrar could seek to do so of their own volition.
NASA's acting president Mark Kia and working committee head Linus Digim'Rina could not be reached for comment but the interim chancellor said they and the boycotting staff had failed to follow the proper complaints process and were not upholding the university's core function of educating students.
"Right now, all lecturers, all staff should go back to work," he said.