"I thought little more about it and went inside and was getting ready. (My press secretary) banged on the door again. He said 'put on your television, another plane has hit the other tower'," he told ABC Radio.
"We knew then it wasn't an accident, it was something worse."
The former prime minister was in the US in September 2001 for a visit that included talks with President George W Bush the day before the deadliest terror attack on American soil.
Mr Howard said the significance of the event soon became apparent.
"It meant a lot to the whole world, and it certainly meant that I quickly came to realise just how important our association with the Americans was, because this powerful country had been attacked in an atrocious, cruel manner," he said.
"It meant that the world would never be the same."
News of a third plane hitting the Pentagon emerged while Mr Howard was holding a press conference, with smoke from the site visible.
Mr Howard was later taken to a bunker at the Australian embassy for his protection as the rest of the day unfolded.
The September 11 attacks were the only time the ANZUS treaty has been invoked, with the idea put to Mr Howard on his plane trip back to Australia by his foreign minister Alexander Downer.
"ANZUS had been really built as a mechanism whereby America would come to our aid or New Zealand's aid if we were attacked,'' while still providing for reciprocity, he said.
"This was clearly an attack on the metropolitan power of the United States. So we decided that what we should do is take advantage of that opportunity, and we invoked it."
A quarter of a century on from the terrorist attack that killed almost 3000 people, Mr Howard said the decision to follow the US into wars in Afghanistan as a result of 9/11 was the right thing to do.
"I was unhappy with aspects of the ultimate withdrawal from Afghanistan. It did look rather chaotic at the time ... overall, I don't have any regrets," he said.
The former prime minister said the attacks were an unparalleled event of his prime ministership, shattering long-held notions for many around the world.
"That was the beginning of it. It was the attacks on the morning of the 11th of September, 2001, that shattered the illusion, if it existed as an illusion, that we lived in a world free of terrorism," he said.
"It was an entirely new and different and horrifying and terrifying world."
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