They were initially charged with forging documents relating to the murder of Munir.
But those charges were dropped and they were then charged with helping commit premeditated murder, Muhammad Assegaf, Setiawan's defence lawyer, said on Sunday.
Munir, who exposed abuse by the Indonesian army during Suharto's rule, died of arsenic poisoning in September 2004 while travelling on Garuda from Jakarta to Amsterdam via Singapore.
Setiawan and Aini, who had been interrogated in an earlier investigation, were named as suspects in the case, left unsolved following the acquittal last year of Pollycarpus Priyanto, an off-duty pilot and the only defendant at the time.
Pollycarpus, who was on the plane, had been sentenced by a lower court to 14 years in prison, but an appeals court later overturned his murder conviction, citing insufficient evidence.
On Friday, police gave the attorney-general's office what they described as new evidence that would merit a judicial review of Pollycarpus' acquittal.
Assegaf, the defence lawyer, criticised the move against Pollycarpus as illegal, saying: "Under Indonesian law, only a defendant ... has the right to appeal for judicial review".
However, Major-General Sisno Adiwinoto, national police spokesman, said the fresh inquiry was partly based on forensic testing in the US that showed Munir was probably poisoned during a stopover in Singapore, 30 to 90 minutes before he died.
Adiwinoto said there was enough evidence to arrest Indra and Rohainil on suspicion of falsifying a letter that enabled Pollycarpus to get aboard the plane.