Geo and Samaa channels, known for critical reporting of the government, were blocked from broadcasting for around an hour.
Government officials were not available for comment. Geo said it had been given no reason.
A message from Pakistan's media regulatory body appeared on those channels announcing it was temporarily suspending transmission of "independent news TV channels" until further notice.
Several other TV news channels also known for their hard-hitting reporting continued to broadcast.
Like other news channels, the stations had been covering.
The military said that two attackers had infiltrated the complex and were holed up inside but that troops had surrounded them.