Noboa was inaugurating a water treatment plant in central Ecuador when his motorcade was set on by a large group protesting rising fuel prices.
“About 500 people showed up and were throwing stones at him, and there are obviously bullet marks on the president’s car as well,” said Environment Minister Ines Manzano.
Video released by the government, reportedly filmed from inside the motorcade, shows protesters standing in the road, draped in flags, scrambling to collect large stones and bricks.
As the presidential SUV passed, projectiles thudded into the panelling and shattered windows.
A voice can be heard shouting, “Heads down! Heads down!” as the vehicle sped away.
Officials said they were still investigating whether some of the impact marks on Noboa’s armoured Chevrolet Suburban were caused by gunfire.
Growing unrest
The attack came amid days of increasingly violent demonstrations sparked by a government decision to raise diesel prices.
Protestors have gone on strike, blocked roads and abducted 16 soldiers – who where eventually released unharmed.
On Sunday, Ecuador’s largest Indigenous organisation reported that a protester had been killed by armed forces during one of the rallies.
Between protestors and security services, more than one hundred people are believed to have been injured in the unrest.
Noboa has declared a state of emergency across several provinces.
The recently re-elected president is trying to cut diesel subsidies to save about US$1 billion in government spending, diverting much of the savings to security funding.
Ecuador, once considered one of Latin America’s safest nations, has seen a dramatic surge in violence in recent years.
Strategically located between Colombia and Peru – two of the world’s largest cocaine producers – Ecuador has become a major transit hub for narcotics.
Authorities have accused drug gangs of fuelling the unrest, suggesting that criminal groups are exploiting the protests to destabilise the country.
It is estimated that 70% of the world’s cocaine supply passes through the country, much of it destined for the United States.
The trade has attracted international criminal organisations, including Mexico’s Sinaloa Cartel, Italy’s ‘Ndrangheta, and Albania’s mafia.
Their competition for control of trafficking routes has turned Ecuador into one of the region’s most dangerous places.
Noboa has called for a referendum to allow the return of US troops to the country, repealing a 2009 ban on foreign bases.