The institute said "obvious" efficiencies from central planning never materialise.
"As someone said, if you introduce central planning to the desert, nothing much will happen at first, but after a while there will be a shortage of sand," the Institute said.
It urges the government to take steps to free up the economy, including the
break-up of export monopolies.
"We would expect our largest corporation to share these aims. Sadly, Fonterra has failed to exercise business leadership, in this case," the Institute said.
Fonterra's competitor Synlait's submission argues that the selection of additional partners to the alliance should be on a non-discretionary open-access basis.
The scope for authorisation should be clearly defined, Synlait said.
"We are not suggesting that Kotahi must offer common pricing for all," Synlait said.
But the proposal must not result in other exporters and importers subsidising better prices and a negotiating vehicle for Fonterra.
Fonterra says shipping capacity to New Zealand has reduced because of a proliferation of vessel-sharing agreements, which are effectively code-sharing arrangements on ships. MSC maintains the only single-carrier service of any scale to this country.