Mr Morrison said reports suggesting otherwise, following Prime Minister Tony Abbott's visit to Jakarta earlier this week, were incorrect.
"There is no change to the government's policy on border protection," he told reporters in Sydney on Friday.
"Our resolve, our policies, our commitments to the task... are indeed stronger than ever before."
Mr Abbott's visit to Indonesia had paved the way for measured discussions with Australia's northern neighbour.
"Everything is on the table," Mr Morrison said, repeating Mr Abbott's commitment to respect Indonesia's sovereignty.
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Mr Morrison said the first team of Australian officials arrived in Jakarta on Friday to start discussions with their Indonesian counterparts.
A high-level delegation, lead by Operation Sovereign Borders acting commander Air Marshal Mark Binskin and including Australian Federal Police commissioner Tony Negus, would follow next week.
Retired major general Jim Molan, who was this week formally appointed as the prime minister's special envoy on asylum seekers, would also attend that meeting.
"Our countries have a long history of co-operation on these issues," Mr Morrison said. "There is much work to be done."
But Mr Morrison said the federal government would not be briefing media on the matters discussed at the bilateral meetings.
"Our dialogue, like our operations, will be undertaken with Indonesia with total discretion to ensure the success of that dialogue," he said.
"They will not ... be undertaken through the media."
Air Marshal Mark Binskin also gave an update on the latest asylum seeker boat arrivals.
The usual briefing, which would have taken place on Monday, was moved up due to the public holiday across Australia on October 7.
Air Marshal Mark Binskin said one asylum seeker boat had arrived this week, on September 30.
It was carrying 79 asylum seekers. The vessel has sought assistance from Australian authorities and the navy had gone to its aid. All those on board were transferred to Christmas Island, along with three crew members.
The asylum seekers will later be transported to centres on Nauru or Papua New Guinea's Manus Island.
Air Marshal Binskin said 334 asylum seekers had been transferred to the offshore processing centres since Operation Sovereign Borders commenced on September 18.
In total, 953 people are being detained in Manus and 801 on Nauru. An additional 43 are in transit. There are 2263 people at the Christmas Island facility.
