While the three-phased local elections are officially being held on a non-party basis, political parties - including the ruling pro-Musharraf Pakistan Muslim League - have openly backed their candidates.
The Muslim League says its candidates fared well in Thursday's voting in all four provinces - just like they did in the first ballot on August 18.
Opposition parties, including an alliance of Islamic groups, are denouncing the elections, saying it is impossible to have a free vote under President Pervez Musharraf.
But the president dismisses such accusations and hails these latest polls as a victory over Islamic extremism.
"The outcome of the elections overall in the country is a victory for the moderates for the enlightened and a defeat for the extremists," said Pervez Musharraf.
The anti-Musharraf Islamic alliance of religious parties, known as Muttahida Majlis-e Amal, has failed to make significant gains in the voting so far - not even in its stronghold of the North West Frontier Province.
The final phase of elections will be held on September 29 in that province, as well as Punjab, Sindh and Baluchistan.
Analysts say a broad win for President Musharraf's allies in these local elections will help him map out his political strategy ahead of the 2007 general elections.
Hassan Askari is a political commentator and former professor of political science at Pakistan's prestigious Punjab University.
"The new presidential elections would be held in 2007 and as the pro-Muslim League candidates have performed better in the local bodies' elections, this would be interpreted as strengthening pro-Musharraf forces," said Hassan Askari.
Since seizing power in a bloodless military coup in 1999, General Musharraf won a five-year term as president through a controversial referendum in 2002. He has since amended the constitution - with parliamentary approval - to allow him to serve as president while remaining military chief.