The rust "looked like metal rust" and it was possible the rubber had been contaminated from metal ribs contained in old tyres.
"There is also some bubbling of the track, and other issues," Mr Hooker said.
He said the track warranty was for five years and was about halfway through.
Mr Hooker said another problem being worked through by the trust was financial.
The track was open all day every day for athletes to train and the trust relied on the honesty of those using the facility to pay.
He said it seemed some regular users, who can get full use of the track for an annual fee that amounts to little more than a dollar a week, were failing to pay at all.
"I had a meeting just recently with Masterton Mayor Lyn Patterson and councillor Mark Harris where we discussed the pressure we are under and how we could make the track more economically viable," Mr Hooker said.
He said the idea of honesty boxes had been toyed with "but they only end up getting broken into. We have had problems with graffiti at the track as it is."
Mr Hooker said at the end of the day it all got back to people's honesty and integrity. The trust was set up to overlook the construction of the track and the idea was to then hand it over to a management trust.
Mr Hooker said this had not come to pass because people were not prepared to "put their hands up" and form a management trust.
"Everyone seems to agree it's a fantastic facility and that there is great potential there but they don't want to accept any responsibility for it."
