ISTANBUL – When Taliban troops seized control of the Afghan capital two weeks ago, the invading units made a beeline for two critical targets: the headquarters of the National Security Directorate and the Ministry of Communications.

Their aim — recounted by two Afghan officials who had been briefed separately on the raid — was to secure the files of Afghan intelligence officers and their informers, and to obtain the means of tracking the telephone numbers of Afghan citizens.

The speed with which Kabul fell on Aug. 15, when President Ashraf Ghani fled, was potentially disastrous for hundreds of thousands of Afghans who had been working to counter the Taliban threat, from prominent officials to midlevel government workers, who have since been forced into hiding.

Few officials found the time to shred documents, and thousands of top secret files and payroll lists fell into enemy hands, the two officials said. As U.S. troops complete their withdrawal by their Tuesday deadline, much of the nation is cringing in fear in anticipation of coming reprisals.

So far, the Taliban's political leadership has presented a moderate face, promising amnesty to government security forces who lay down their arms, even writing letters of guarantee that they will not be pursued, although reserving the right to prosecute serious crimes. Taliban spokespeople have also talked of forming an inclusive government.

Spokesman Suhail Shaheen said on Twitter that there was no settling of scores nor was there a hit list with which the Taliban were conducting door to door searches, as has been rumored. "General amnesty has been granted," he wrote, "we are focusing on the future."

Yet there are growing reports of detentions, disappearances and even executions of officials at the hands of the Taliban in what some current and former government officials describe as a covert and sometimes deadly pursuit of Taliban enemies.

"It's very much underground," said one former legislator who was in hiding elsewhere when the Taliban visited his home in the middle of the night. "That is intimidation," he said. "I feel threatened and my family is in shock."

The Taliban swept into towns and districts, often without a shot fired, making diplomatic assurances to their foes and the public. But the first commanders have often been replaced by more heavy-handed enforcers who conduct raids and abductions, former government officials said.

The scale of the campaign is unclear since it is being conducted covertly, nor is it clear what level of the Taliban leadership authorized detentions or executions.

The people who seized the files at the National Security Directorate and the Ministry of Communications may not have even been Taliban: the men did not speak Afghan languages, the officials said, and may have been agents of Pakistan's military intelligence agency working in tandem with Taliban forces. Pakistan's Inter-Services Intelligence agency has long supported the Taliban in their violent opposition to the Kabul government.

The fear among Afghans is palpable. All but the youngest remember the authoritarian regime of the 1990s, with its draconian punishments, hangings and public executions.

Many people have gone into hiding, changed their locations and telephone numbers, and broken off communications with friends and colleagues.

"People do not trust the Taliban because of what they did previously," said an Afghan who worked as a translator for the NATO mission and was among those evacuated.

Human rights organizations, activists and former government officials have also struggled to comprehend exactly what is happening across Afghanistan's vast mountainous terrain, but several government officials who remain in their posts said they were receiving increasingly frantic calls from relatives and acquaintances.

"They seem to be doing very menacing searches," said Patricia Gossman, associate Asia director for Human Rights Watch. "It is very much police-state kind of behavior. The message is very clear."

People in northern Badakhshan Province have been pulled out of their homes and have not been seen since, one of the government officials said. There has been a pattern of pursuit of Afghan special operations forces personnel and commandos of the intelligence service, known as 00 units, as well as police and security chiefs.

The former security police chief in southwestern Farah Province, Ghulam Sakhi Akbari, was fatally shot on the main Kabul-Kandahar highway Friday, according to Facebook posts by activists.

At least a dozen former provincial officials of the Ghani government have been detained by the Taliban, former government officials said. They named three district police chiefs and three security officials in southern Kandahar Province, two provincial police chiefs, a provincial governor and two provincial department heads of the intelligence service, all of whom are known to have been detained.

It is not clear where the officials are being held or if any legal proceedings have been brought. In some cases, they have been reported missing by family. In the case of the three district police chiefs in Kandahar, members of the public had demanded that the Taliban arrest the men, who have long been accused of human rights abuses, a resident said.

Some political activists have raised concerns that some of their supporters are missing and feared abducted.

One activist, Majeed Karar, who is well known for his opposition to the Taliban, posted photos of a district governor and a young Afghan poet whom he said had been abducted and killed. He said that he was receiving messages from friends about more killings.

The Taliban have not confirmed the detentions and, seemingly intent on avoiding international censure, have blamed some violence on others claiming to be Taliban.