The Shenzhen Federation of Trade Union became involved after the company announced it would eliminate a layer of management in all its stores, leaving affected employees the option of taking a lower position with lower pay, Xinhua news agency said.
Wal-Mart's China unit, based in southern Shenzhen, has 147 outlets and over 50,000 employees.
The company will give a one-off reward of 3,000 yuan ($440) to those who agree to be transferred to work in other stores, or receive training offered by the company, Wang Tongxin, vice chairman of the union, was cited by Xinhua as saying.
After talks with the employee representatives, Wal-Mart has taken the concerns of the employees and made big revisions to its plan, which finally reached a win-win situation, said Wang.
An official from the company also confirmed the news.
After revision, our program is going well. A growing number of employees understood the company's strategy and are willing to accept the arrangement, Chen Lu, a Wal-Mart China public relations official, was quoted as saying.
Wal-Mart first allowed unions into its Chinese stores in 2006, during a government campaign to expand the presence of unions into foreign multinationals.
But Xinhua quoted some employees as saying it would take time to rebuild trust.
We are not sure now whether the company can keep its promise, an anonymous Wal-Mart manager in Shenzhen was quoted as saying.
(Reporting by Beijing newsroom; Editing by Nick Macfie)