Even some Taliban fighters now regret the disruptions and are demanding that service be restored by the companies.
The communication blackout follows a campaign by the Taliban, which said the U.S. and NATO were using the fighters' cell phone signals to track them at night and launch pinpoint attacks.
About 10 towers have been attacked since the warning late last month - seven of them seriously - causing almost $2 million in damage, the telecom ministry said. Afghanistan's four major mobile phone companies began cutting service across the south soon after.
The speed with which the companies acted shows how little influence the government has in remote areas and how just a few attacks can cripple a basic service and a booming, profitable industry. The shutdown could also stifle international investment in the country during a time of rising violence.
But the cutoff is proving extremely unpopular among Afghan citizens. Even some Taliban fighters are asking that the towers be switched back on, said Afghanistan's telecommunications minister, A. Sangin.
That dissenting view shows how decisions made by the top-ranking Taliban leadership can have negative consequences for lower-ranking fighters in the field, the minister said.
Taliban spokesman Zabiullah Mujahid hinted in a telephone interview that the group could change its tactics.
"We see that some people are having problems, so we might change the times that the networks are shut down in the coming days," Mujahid said.
That the Taliban could dictate when the country's mobile phone networks operate shows the weakness of the central government and the international forces that operate here, said Mohammad Qassim Akhgar, a political analyst in Kabul.
"After the Taliban announcement, they were aware of the situation, and still they couldn't provide security for the towers," Akhgar said. "Maybe destroying a few towers will not have any effect on the government, but the news or the message that comes out of this is very big, and all to the benefit of the Taliban."
All four of the major phone companies - Roshan, AWCC, Areeba and Etsalat - declined to comment.
Sangin said the government is not overly worried about the Taliban threat because Afghans are becoming increasingly angered by the shutdown. He said seven destroyed towers, and three others with minor damage, out of the 2,000 now in the country was "not a big thing," though he added that the towers cost from $150,000 to $300,000 each.
"Our view of the people targeting the telecom infrastructure is that it's not a fight against the foreign troops, it's not a fight against the government, it's actually targeting the people, because the result of such activities is that the people will suffer," Sangin said. "We believe the people will stand up and provide protection for the telecom towers."
Haji Jan Ahmed Aqa, a 45-year-old farmer from the remote and dangerous Zhari district of Kandahar province, said the loss of cell phone communication at night is a big problem.
"What do we do if someone is sick?" he asked. "How can you agree to this Taliban demand? Maybe next the Taliban will say they have a problem in the daytime, and they'll shut down the network at daytime as well."
Afghanistan's cell phone industry has seen explosive growth since towers first appeared in late 2002, Sangin said. The country now has 5.4 million cell phone users and the industry has invested more than $1 billion. Sangin said he expects another $500 million in investments over the next two years.
Attacks on towers have taken place across the south, where the Taliban is most active. Companies have shut down service primarily in Helmand, Kandahar and Zabul provinces.
An official with knowledge of the situation said about 10 percent of the country's towers were being turned off at night, affecting up to 300,000 people. He spoke on condition he not be identified because he wasn't authorized to release that information.
The shutdown, Sangin noted, is causing problems both for civilians and for militants.
"In these provinces I've actually received reports where the Taliban has gone to some towers and told the companies not to shut them down, and keep them running," said Sangin. "I get the feeling that they are already regretting their decision to shut down the services."
Simon Baker, a Moscow-based analyst with the telecommunication firm IDC, said that despite the attacks, the outlook for the telecom industry in Afghanistan is still "pretty good," given the country's large untapped user base.
"There are substantial amounts of capital behind it. I think people will try to find a solution to this," Baker said. "Major international players will take the longer term view."
Sangin said the Taliban's stated reason for wanting the networks shut down - because the U.S. and NATO can track militants' movements - doesn't make sense, because the fighters could simply turn their phones off or remove the batteries. He said the military has other ways to track the militants.
U.S. Ambassador William Wood told reporters last month that the threat could cause investors to hesitate.
"I don't think that it's a serious threat because the Taliban relies on cell phones, too," Wood said. "But you can see how that would be a problem for a private investor."
Sangin, the telecommunications minister, said the Taliban closed down a cell tower in Ghazni province about four months ago, but that villagers demanded it reopen.
"The people said please ... repair the infrastructure and we will guarantee the security of the tower," Sangin said. "We believe that if the Taliban continue with these kinds of activities the hatred will increase against them, and as a result we are awaiting a change in their policy."