India's Prime Minister Narendra Modi has used a telephone call with Prime Minister Malcolm Turnbull to personally voice his reservations about the Federal Government's decision to scrap the 457 visa.

India was upset by the Government's announcement last month that it was replacing the 457 visa for temporary skilled workers with two new visas.

In its place will be a two-year visa and a more specialised one for four years "targeted at higher skills".

Mr Turnbull said the changes were "in the national interest".

Indian nationals account for a quarter of 457 visa holders, the most of any nationality.

India had hinted the move to replace it could affect trade negotiations, which the two countries had only just pledged to revive during Mr Turnbull's recent India visit.

Now, according to India's Ministry of External Affairs, Mr Modi himself has "expressed concern" to Mr Turnbull about the possible impact of visa changes.

India said yesterday's phone call was initiated by Mr Turnbull.

In a statement, India's Ministry of External Affairs (MEA) said that the two leaders agreed that "officials from both sides will remain in close touch on the issue".

Indian workers are not likely to be severely affected however, because the technology and chef roles they mostly fill will still be eligible under new visas.

India has already acknowledged it knows that to be the case.

MEA spokesman Gopal Baglay told the ABC last month that "we also understand, because the Australian senior officials have told us, that the impact on the Indian IT professionals will be negligible".

The Prime Minister's Office and Department of Foreign Affairs and Trade have been contacted for comment.