The Central Bureau of Investigation has charged Pandher only with destruction of evidence. Koli has been charged with murder, rape and necrophilia.
The CBI said the prosperous businessman had tried to help Koli because he took good care of him.
"Pandher was unaware of the heinous acts of Surender," Arun Kumar, CBI joint director, said.
Virtually putting the blame on Koli for the murders, the CBI said he had carried out the crimes while his employer was away from his home in Noida in the outskirts of New Delhi.