He said the Malaysia deal was designed to do "exactly" that, "creating safer pathways, increasing the humanitarian intake", The Age newspaper quoted the minister as saying.
Bowen told ABC Radio today he had argued consistently that if the Malaysia deal was blocked, there would be more deaths at sea.
"I've never been more disappointed to be proven right. This is a terrible tragedy but it's a fact that when you've more boats coming to Australia, you'll see more deaths.
"We didn't adopt the Malaysia arrangement because it was politically easy or it was convenient, quite the opposite.
"We adopted it because we knew that this was the sort of arrangement that was necessary, to prevent more deaths at sea, and that's exactly what we've seen," he said.
However, he stopped short of openly blaming the opposition which has refused to pass legislation to overcome the court ban on the Malaysia swap deal in Parliament.
Bowen also said the arrival of another boat carrying 92 asylum seekers off Christmas Island yesterday, the sixth since the policy shift to onshore processing, showed there had been an "uptake of boat arrivals" since the Malaysia deal collapsed, which the government had also predicted.
Opposition immigration spokesman Scott Morrison said the government could have its legislation clear Parliament if it accepted opposition amendments.
But, he refused to blame government policy for the drowning deaths. "It's unhelpful to engage in that sort of rhetoric," he told ABC Radio, adding that criminal people smugglers were to blame.