"There is no impropriety on the part of Usec Puno when he assumed the functions of the DILG usec for peace and order directly in charge of the PNP affairs pursuant to the order of the President," the Palace report said.
The IIRC had singled out Lim for both administrative and criminal liability for the fiasco that sparked outrage in China and Hong Kong and strained diplomatic relations between Beijing and Manila.
The committee had recommended administrative sanctions against 12 other people and recommended that they face preliminary investigation by appropriate agencies to determine if criminal cases against them are warranted.
But Mr Aquino, adopting the recommendations of his legal team headed by Executive Secretary Paquito Ochoa and Chief Legal Counsel Eduardo de Mesa, simply called for administrative charges against Lim and six other officials.
"I pledged from the very start that there would be accountability," said Mr Aquino, who had put off several times the announcement of his actions against those liable.
"The purpose of the review was to find the viable legal actions which can be taken against the concerned parties," he told reporters. He said he wanted to avoid "frivolous lawsuits."