Craig McMillan said that issue is players picking and choosing when to play for New Zealand.
Last August, Boult opted out of his New Zealand central contract to spend more time with his family and continue playing franchise cricket throughout the world. Boult will play in the inaugural season of the United States' Major League Cricket, which begins next month.
The 33-year-old left-arm pacer was not on NZC's most recent central contract list, which was released last week, but the board offered him a casual playing arrangement.
Hesson termed the said agreement a big untidy and mentioned that the players need to decide to play the IPL and also 2-3 other tournaments at the start of the year itself.
"If you want the IPL and two or three or four other tournaments as well, you probably can't have everything and that's a decision you've got to make at the start of the year and I just think the flexi contracts just make it a bit untidy.
It just gets untidy when you've got 20 contracts or however many are on that (NZC) list now and then you have an extra one (for Boult) and next year you might have three extra ones and it just gets untidy,” Hesson said on Sky Sports.
Boult who was part of the New Zealand side in the T20 World Cup 2022, will most likely be part of the Black Caps squad for the 2023 ODI World Cup in India.
Hesson feels NZC would soon face a situation where it will have to offer different contracts to different cricketers depending on their circumstances, with the growing number of T20 leagues.
"Under the current (NZC) model it doesn't. You get ranked in three different forms and you add the points up and that's your number everyone has known that and it's worked pretty well for an extended period.
This flexi contract might work well for Trent and it might work well for New Zealand Cricket, but it does open up a whole can of worms," Hesson said.
"It seemed only 12 months ago Trent Boult was more than happy to make his decision to move away from international cricket and take the riches of the T20 franchises around the world and you couldn't bemoan him that.
He'd had a wonderful career for New Zealand and been a great servant and now almost wants a little bit of a dollar each way. It's a difficult one,” McMillan said.
For McMillan, who is a former New Zealand assistant coach as well, the problem arises when players are coming back and trying to pick and choose when they play international cricket for New Zealand.
"It doesn't sit overly well with me and I'm sure it doesn't sit with some of the other players within the setup who are doing the hard yards then have to move back (when they return)," McMillan added.
(PTI inputs)