"Interior removals", which are deportations after being arrested away from the border, increased 25 percent.
The administration has said its immigration policies emphasize national security but there is no indication that a higher rate of unsafe criminals are being apprehended, detained or deported, compared to under Barack Obama.
Overall, the agency reports HSI made 32,958 criminal arrests and seized $524 million in illicit currency and assets after investigating cross-border criminal activity in FY17.
"The president made it clear in his executive orders: There's no population off the table", Thomas Homan, ICE's acting director, told reporters in Washington on Tuesday.
"We're bankrolling criminal organizations, we're enticing more people into this country and it's a public safety threat", Homan said. ICE says that the total number of removals nationwide was down 6 percent this year compared to last year, which the agency attributed "to the decline in border apprehensions".
In March, former Homeland Security Secretary John Kelly testified to Congress that fewer than 17,000 people had been arrested along the southern border that month.
DHS said 92% of people Ice arrested from the inauguration through September "had a criminal conviction or a pending criminal charge, were an Ice fugitive or were an illegal re-entrant".More news: John Travolta film cancelled a week before release
Much of the period covers the time after Mr Trump's United States election victory in November 2016, following his campaign pledge to build a wall along the Mexican border. As president, he has signed a series of travel bans aimed at curtailing who can enter the country, pushed to overhaul the legal immigration system and tried to crack down on so-called sanctuary cities that refuse to share information about illegal immigrants with federal authorities. But officials insisted the wall was still needed. "We're still arresting almost 1,000 people a day coming across the border", he said.
"The fact that we're still seeing these vulnerable asylum seekers make the journey to the United States is strong evidence that they are genuine refugees and they do need humanitarian protection in the United States", she said.
"The administration can try to twist these numbers into whatever they please", he said.
Although Homeland Security officials touted the overall drop in arrests, they did note that, since May, arrest had ticked up, mainly because of families and unaccompanied children from Central America trying to escape violence and instability caused by fighting between drug cartels, a yearslong trend.
The actual number of illegal borders crossings isn't known because many people slip in undetected.
On Tuesday DHS took a much harsher position on such people, suggesting they abuse U.S. immigration laws and pose a threat to the US. AP writer Anita Snow contributed from Nogales, Mexico.