One Square Meal beverages and cereal are also being developed.
Cookie Time said while patents based on manufacturing processes were common, those that created a new class of food and beverage were rare.
Although Booth would not disclose the meal replacement bar's revenue, he said the product had seen double-digit sales growth every year.
Cookie Time said it had also submitted a raft of similar patent applications overseas, including in Britain, the US and Australia.
The bar has been manufactured under licence by Sanitarium across the Tasman since January and Booth said the company was working to secure similar licensing agreements in other countries.
Jason Rogers, a partner with James & Wells Intellectual Property who worked on securing the patent, said it had been a challenging process as it involved "a shift in mindset".
He said many people, including patent examiners, were aware of the term "nutritionally balanced".
But it was misunderstood as it was often used when marketing products that were not actually nutritionally balanced, Rogers said.