Zaki Daryabi, founder and editor-in-chief of the Etilaat Roz newspaper, shared images on social media of two male reporters, one with large, red welts across his lower back and legs and the other with similar marks on his shoulder and arm.
Both men's faces were also bruised and cut in the pictures, which were verified by Reuters.
Daryabi said the beatings sent a chilling message to the media in Afghanistan, where an independent press, much of it funded by Western donors, has flourished in the last 20 years.
"Five colleagues were kept in a detention centre for more than 4 hours, and during these four hours two of our colleagues were beaten and tortured brutally," he told Reuters on Thursday, the day after the incident.
He said the injured reporters were taken to hospital and advised by doctors to take two weeks' rest.
But incidents of abuse since they came to power have raised doubts among some Afghans.
Taqi Daryabi, one of the two Etilaat Roz journalists, said seven or eight people beat them for about 10 minutes.
"They would raise sticks and beat us with all of their strength. After they beat us, they saw that we had passed out. They took us to lock us up in a cell with a few others," he said. Reuters could not independently verify his account.
The last time the Taliban ruled the country from 1996-2001 there was no independent media and the Internet was in its infancy.
Several journalists have complained of assault since the Taliban returned to power, and some women have said they were not allowed to carry on working in media jobs.
"With the sudden collapse of the government, Etilaat Roz initially decided to stay and operate in the hope that there would be no big issue for media and journalists," Daryabi said.
"But with the yesterday's incident, that little hope I had for the future of media and journalists in country is destroyed."