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The Black Stars suffered a disappointing defeat to Cape Verde in their opening game of the 2023 Africa Cup of Nations (AFCON) on Sunday.
A lackluster performance saw the Black Stars fall behind after just 17 minutes following Jamiro Monteiro's rebound.
Ghana bounced back in the second half through Alexandre Djiku’s header and, for a moment, it looked like the night could belong to them.
However, Cape Verde stunned them late in the game, with Garry Rodrigues taking advantage of a defensive mix-up to score the winner.
This leaves Hughton and his side with just one win in their last six matches ahead of their second group game against Egypt on Thursday.
While the Ghana coach has been under huge pressure and was even verbally abused by a supporter at the team’s hotel lobby, the GFA insists Hughton retains their utmost trust.
"We have had a meeting with the coach and gave him 100% assurance that we are solidly behind him," GFA’s spokesperson Henry Asante-Twum told BBC Sport.
"We think it is possible for the team to win the two remaining matches to make it to the next round."
On the chaos that ensued after a fan confronted Hughton, Asante-Twum said: "There was only a verbal confrontation. He was actually trying to get closer to the coach and then the security on duty intervened - there was no arrest but security took him away from the scene.
"Normally after games, tempers are high, emotions go up - we will try as much as possible to not allow this thing to repeat itself."
The Black Stars will be desperate to salvage their AFCON when they face Egypt next.