This comes as US and Taliban officials appear close to an agreement, including on counter-terrorism assurances and troop withdrawal.
Some US officials and lawmakers have warned that a complete pullout would erode the US ability to thwart attacks from Afghanistan.
On August 16, senior US officials held a meeting with President Donald Trump on negotiations, but Bolton was not initially invited to the meeting.
Citing unnamed officials, Washington Post said that the Bolton was not invited out of concern that his team would oppose the agenda and leak the details later. Bolton rejected the allegation.
“I categorically deny leaks by me or anyone authorized to speak to the press. Those alleging such leaks should look in the mirror.”
During the meeting, Bolton and Trump exchanged opposing views over policy options on Afghanistan, it is reported.
Reports also suggest that Bolton asked for a copy of the draft agreement the US is trying to strike with the Taliban, but the US negotiator Zalmay Khalilzad denied the request.
Khalilzad reportedly said that Bolton could read the agreement in the presence of a senior official but not leave with it in hand.
The Taliban have demanded full withdrawal of foreign troops from Afghanistan.
Speaking in an interview on Fox News Radio on August 29, Trump said troop levels would fall to around 8,600 “and then we make a determination from there.”
“We’re going to keep a presence there. We’re reducing that presence very substantially and we’re going to always have a presence. We’re going to have high intelligence,” he added.