Police chief of Paktika province Dawlat Khan Zadran told BBC that the arrested Afghans were members of Haqqani militant network.
Two Kalashnikovs, a motorbike and explosives were seized from their possession.
Zadran said they have confessed to the crime.
Indian author Sushmita Banerjee, who wrote a book about her dramatic escape from the Taliban 18 years ago, was shot dead in Afghanistan on Sept 5.
The 49-year-old author was killed outside her home in Paktika province.
According to BBC reports, the miscreants arrived at her home and tied up her husband and other family members. They took Banerjee out and shot her.
Her body was reportedly dumped near a religious school.
No group claimed responsibility for the attack.
She was married to an Afghan businessman Jaanbaz Khan.
She had penned down her experience with her husband in Afghanistan and her dramatic escape in 1995 in a book called "KabuliwalarBangali Bou" (A Kabuliwala's Bengali Wife).
The book became a best-seller in India and was made into a Bollywood film called "Escape From Taliban" in 2003.
Banerjee had recently moved back to Afghanistan to live with her husband.
--IBNS (Posted on 10-09-2013)