The US personnel have been barred from leaving Pakistan because of expired visas and other documentary irregularities, the Dawn newspaper quoted unnamed sources as saying.
There are varying claims about the number of US soldiers denied exit. Some sources claimed about 20 to 30 people had been affected while others put the figure at slightly less than 100.
The personnel were assigned to the US Office of Defence Representative in Pakistan (ODRP), which oversees bilateral military relations, including training and equipment.
Most of the personnel had been working on different projects with the Pakistani military.
Some of the personnel overstayed their visas while a majority of them had expired no-objection certificates (NOCs).
US personnel posted in Pakistan are issued NOCs by the Joint Services Headquarters that cover the period of their assignment.
The NOCs are meant for visa purposes but the daily quoted its sources as saying that the personnel had stayed in Pakistan beyond the approved period and some of them had got their visas extended without current NOCs.
The issue has been discussed by Pakistan''s Foreign Office and the US embassy but a resolution is "nowhere in sight", the report said.
The Foreign Office was tight-lipped on the matter because of its "sensitive nature".
A US military spokesman admitted that there were problems.
"ODRP and the embassy have been in discussions with Pakistani authorities over visa renewals. We hope to be able to work through this issue," he said, but did not reply to queries about how seriously the matter is affecting already strained bilateral ties and what measures were being taken to resolve it.
An unnamed Pakistani military official tried to play down the matter and said: "These are procedural issues."
Pakistan and the US have not yet been able to "come out of the distrust" that followed the detention of CIA operative Raymond Davis, the report said.
The ISI and CIA had got down to reshaping their relationship before Davis'' release by addressing some thorny matters like "complaints about US arrogance or heavy-handed approach in dealings with Pakistan," the report said.
Shortly after Davis was freed last month under a "blood money" deal whereby over USD 2.3 million was paid to families of the two men he killed, CIA-operated drones fired missiles at a tribal gathering in North Waziristan that killed some 40 people.
Pakistan pulled out of a trilateral ministerial meeting on Afghanistan to protest the drone strikes and called for revisiting the fundamentals of the relationship.
Pakistani security agencies were directed to get tough with the Americans.
In addition to the strong application of immigration rules, the movements of the US embassy''s non-diplomatic staff outside Islamabad and their station of duty have been restricted.
A revision of the visa policy is on the cards.
Foreign Secretary Salman Bashir is likely to visit Washington later this month to discuss measures to revive the dysfunctional relationship, the report said.