Police Inspector Willie Taylor told Radio New Zealand SH1 had been closed between Waiouru and Rangipo.
"It's quite a major crash scene which hasn't affected SH1 itself, but we've been forced to close off the road so we can have a descent investigation of the site and start a search for the missing driver."
He said the initial emergency call was from a motorist who discovered some debris near the stream.
Further investigation by another motorist revealed the partly submerged truck.
Mr Taylor said there were "all sorts of possibilities" as to what could have happened to the driver.
"The stream is quite swiftly flowing and of some volume. The truck has sustained substantial damage and we've been unable to gain access fully to its cab, so there's many unknowns at this stage."
He said police were aware of the importance of the stream, which flows into the Tongariro River and north to Lake Taupo. He understood substances were still escaping from the vehicle.
"We're taking every precaution," he said.
"Due to the remote nature of the site its going to take some time to get the relevant agencies along there with appropriate equipment and make things happen.
He said it was not known what had led to the crash.
"It's a tricky area of the road. There's been some medium-to-cold temperatures overnight. As we all know the Desert Road and the roads surrounding it do get black ice and other forms of ice on them sometimes, and its also on ... a bend that would cause problems if taken at the wrong angle or at speed."
Genesis Energy spokesman Richard Gordon said the Rangipo Power Station had been closed as a result of the crash.
The 120 megawatt power station, which generates enough electricity to power about 100,000 homes, turned its turbines off about 7.30am.
"We're not sure at this stage what material is in the river from the truck crash and we're taking a precautionary approach. We've got intake screens to take large things going through into the Rangipo turbines but we're not sure what material was on the truck."
Mr Gordon said it was unclear when the power station could reopen.
- APNZ