Security chief General Daulat Khan told the Afghan Islamic Press the fighters, armed with machine guns and rocket launchers, had attacked government forces in Paktika province on Tuesday and Wednesday.
He said: "We besieged them in a madrassa (on Thursday)... The local elders were pressing us not to launch any attack, but we have told them that we will definitely search the madrassa."
Some of the Taliban managed to flee on their motorbikes, Khan added, describing the situation as tense.
Paktika, bordering Pakistan, is one of the main battlegrounds of a resurgence by Taliban fighters and their supporters in the their former strongholds in southeast Afghanistan.
The resistance fighters have targetted troops and officials in a campaign to destabilise the US-appointed President Hamid Karzai.
The fighting came a day after aid agencies warned that reconstruction work in some areas of the battered country was almost impossible due to the deteriorating security situation.
"Since September 2002, armed attacks against the assistance community have increased from one a month to an average of one every two days," international aid agency CARE said in a statement.
The Taliban's 1996-2001 government was overthrown in a US-led military campaign in the aftermath of the September 11 attacks on New York and Washington.