Stormont’s Infrastructure Minister, Nichola Mallon, said two masked men “muttered something about the protocol” as they held the driver at gunpoint.
The incident happened in the Abbot Drive area of Newtownards at about 6.30am on Monday.
Two masked and armed men boarded the bus and poured fuel over the vehicle before setting it alight.
The driver managed to get off the vehicle unharmed but has been left badly shaken by the incident. No passengers were on board at the time.
The charred and smouldering shell of the vehicle remained in the area on Monday afternoon. A nearby bus shelter was also significantly damage by the blaze.
The attack in the predominantly unionist area happened on the day set by the DUP earlier in the autumn to pull down the institutions at Stormont if major changes to the protocol had not been secured.
The DUP has not yet withdrawn ministers from the Executive, insisting progress is being made in efforts to dismantle the contentious Irish Sea border.
Opposition to the arrangements that have created trade barriers between Northern Ireland and the rest of the UK was a factor behind rioting that flared in several loyalist areas across the region in April.
Ms Mallon told BBC Radio Ulster’s The Nolan Show: “Two masked men entered the bus. They held the driver, a male, at gunpoint, they said something about the protocol, and they then proceeded to spray the inside of the bus with flammable liquid. They forced the bus driver off the bus and then they set it alight.
“The faceless, mindless cowards who did this have done nothing more than attack their own community.”
She added: “We understand that they muttered something about the protocol.
“I do not know what these people thought they were setting out to achieve by putting at risk a bus driver just trying to do his job and attacking a bus that is there to transport people in the community. It is mindless.”
Bus services in area have been temporarily suspended following the attack.
DUP leader Sir Jeffrey Donaldson said: “There was never any justification for masked gunmen on the streets of Northern Ireland and there never will be.
“When I outlined DUP action on the protocol at the start of September, I indicated that action was needed within weeks. At that time the European Union was saying that fresh negotiations were impossible.
“Since then the EU have agreed to table fresh proposals and serious negotiations have reopened with the UK Government.
“No reasonable person could deny that this represents significant and positive progress. That progress was secured through political action and not violence.”
He added: “Our focus should be on restoring Northern Ireland’s place fully within the UK internal market.
“If the EU refuses to agree to the restoration of Northern Ireland’s constitutional and economic integrity then it will fall to the UK Government to meet its commitment in the NDNA (New Decade, New Approach) agreement to do so through UK legislation.
“That is the road map to securing removal of the Irish Sea border. Those engaging in thuggery only undermine these efforts and cement the protocol more firmly in place.”
Ulster Unionist leader Doug Beattie tweeted: “Utterly disgraceful, depressing and stupid actions of thugs and criminals. In what way does this help address issues concerning the protocol, it simply hurts their own community. Wise up.”
Unite the union also condemned the attack.
Deputy regional secretary Davy Thompson said: “Today our thoughts are with the driver and his family, who will no doubt be very shaken by his experiences this morning.
“This is a bus driver, out doing his best to provide for his family, exposed to the unbelievable horror of being removed from his bus, then watching it burn whilst a local community were left with disruption to their transport links, affecting the ability to get to appointments, school and work.
“This attack is indefensible and wrong. It served no purpose aside from traumatising a worker and undermining access to public transport for a local community.”
He added: “We would call on all those who may have influence in our society to do all they can to ensure that these types of incidents are ended.”