It will mean he will not be opened up to questions from media, including about West Papua.
In a statement, West Papua Action Auckland urged Ardern to raise human rights and the "suffering of the people of Indonesian-ruled West Papua" with Widodo.
"West Papuan people have been seeking freedom from repressive military rule. The loss of life is estimated to be at least 100,000.
"Our Melanesian neighbours in West Papua are suffering grievously and must not be overlooked for the sake of 'good relations', or markets for our goods."
Vietnamese Prime Minister Nguyễn Xuân Phúc, who met with Ardern on Tuesday, also did not hold a press conference with Ardern.
Widodo has been at an Asean meeting in Australia and first met Ardern at the East Asia Summit last year.
He will be welcomed at Government House on Monday before having lunch with Governor-General Dame Patsy Reddy.
He will then meet with Ardern, and afterwards with Opposition leader Simon Bridges.
Trade is expected to be high on the agenda; a booming population and consumer class make Indonesia an important market for New Zealand.
New Zealand and Indonesia have free trade through New Zealand's trade agreement with Asean, but in 2013 New Zealand took Indonesia to the World Trade Organisation over 18 agricultural trade barriers.
According to the Ministry of Foreign Affairs and Trade, the barriers are estimated to have cost the New Zealand beef sector up to a billion dollars, and have also affected horticultural exports.
Indonesia appealed a decision in New Zealand's favour in 2016, and the WTO upheld its ruling in November last year that the 18 barriers were inconsistent with global trade rules.
Trade Minister David Parker said at the time of the ruling that it would open the way for further export growth to Indonesia.