Helicopter gunships fired on the Taliban strongholds of Makeen and Ladha on Wednesday, security officials have said.
They added that gun battles had taken place in Kotkai, the birthplace of Hakimullah Mehsud, the Pakistani Taliban chief.
But Imran Khan, Al Jazeera's correspondent in Islamabad, Pakistan's capital, said the Taliban has denied reports that its fighters have lost control of Kotkai.
"The Taliban are saying that Kotkai has not been secured by the Pakistani army. The Pakistani army sources through the local media say 'yes it has'. So we have this information battle going on."
The offensive in South Waziristan, which began on Saturday, is being followed closely by Western powers involved in the fight against the Taliban in Afghanistan.
It is being seen as a major test of the Pakistani government's ability to tackle fighters who have carried out attacks across Pakistan, killing at least 150 people in a string of suicide and bomb attacks in recent weeks.
Pakistan's military has also called on Nato troops in Afghanistan to seal the border between the two countries "to prevent cross-border movement and flow of weapons".
General Tariq Majid, chairman of the Pakistan Joint Chiefs of Staff Committee (JCSC) made the call during talks with Sir Jock Stirrup, Britain's chief of defence staff, on Tuesday.
Majid called for "synchronisation of effort on both sides and sharing of real-time intelligence with reference to the ongoing operations,"
About 28,000 soldiers are battling an estimated 10,000 Taliban fighters, including about 1,000 Uzbek fighters and some Arab al-Qaeda members.
More than 100,000 civilians have fled from South Waziristan, with about 32,000 of them leaving since October 13, the United Nations said.
The army says up to 200,000 could flee the region.
Source: Al Jazeera (English)