The measure would prohibit the sale of alternative nicotine and vapor products like e-cigarettes to minors under the age of 18 years.
But the bill would also exempt those products from being regulated like traditional tobacco products.
The bill passed with bipartisan support last spring.
In his veto letter, Nixon cited the de-regulation provision for his veto.
"This bill, which is supported by sellers of such products and at least one major tobacco manufacturer but is opposed by leading health organizations, creates a facade of regulation and is actually harmful to Missourians becuase of the special exemptions it provides for these dangerous products," Nixon wrote.
The American Cancer Society Cancer Action Network of Missouri opposes the bill.
"Basically we feel that it does not protect Missourians' health the way it's currently written and so our concern is just that it's going to you know kind of lend itself to hooking a new generation of tobacco for our children," ACS CAN spokesperson Stephanie Reliford said.
Rep. Caleb Rowden, R-Columbia, said the most important part of the bill is the age restriction, not the regulation provision. He introduced the House version of the bill last spring.
"At the end of the day I think this bill protects minors from potential exposure to e-cigarettes before they are legally old enough to make the determination as to whether it's good for them or not," Rowden said.
Rowden also said the governor's motivation for vetoing the bill was mainly political.
"The governor decided to engage in a blatantly political game and in doing so you know potentially harmed and endangered minors in Missouri, and that's unfortunate," Rowden said.