Melissa Lee has been stripped of her media portfolio and sacked from cabinet, while Penny Simmonds has lost the disability ministry.
Mr Luxon said the pair remained "good, hardworking ministers that are valued" but were victims of difficult circumstance.
"I want to make sure I've got all my aces in their places," he said.
"The way that I roll, the way that I lead teams, is I make sure that I have my people in the right places and make sure that they are the right person on the right assignment at the right time.
"These portfolios have gotten more complex.
"As a result, I want senior cabinet ministers who have adjacent portfolio responsibilities that are linked to these these portfolios, taking responsibility for it."
Ms Lee in particular had endured a torrid time as media minister, struggling to articulate the government's response to the closure of Newshub, New Zealand's only commercial television news operation.
Ms Lee battled through a number of trainwreck interviews following Newshub's shutdown, which will bring hundreds of job losses and hurt media diversity.
She will be replaced by Paul Goldsmith, a close ally of Mr Luxon, who the prime minister said would benefit from "synergies" between his existing arts and culture portfolio and his new media role.
Ms Simmonds also drew sharp criticism from carers and a wave of negative headlines when her ministry announced - without consultation - it planned to cut respite funding.
The disability portfolio has been handed to Louise Upston, already social development minister.
With the benefit of a free spot in cabinet, Mr Luxon has elevated Simon Watts, fulfilling at his second attempt a campaign pledge to ensure the climate change minister sat around the cabinet table.
The changes come five months - to the day - since Mr Luxon announced his first ministry, which includes members from three parties: his centre-right National party, the right-wing libertarians ACT and populists NZ First.
Mr Luxon said neither coalition partner had raised issues with the performance of Ms Lee or Ms Simmonds.
"The reason why we're having this change is because these portfolios have evolved and they have become more complex as a result," he said.
"I'm just a person who will adapt very quickly and dynamically to changing circumstances and situations.
"I appreciate that may not be the way things have been done in the past here but expect the same thing going forward."
Opposition leader Chris Hipkins said the early reshuffle showed the coalition was chaotic behind the scenes.
"It shows he clearly didn't have particularly good judgment if he's sacking them so soon after making them ministers," he said.
Mr Hipkins said Ms Upston should begin her tenure by apologising to the disability community for "derogatory" comments made by Ms Simmonds to carers.
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