ESPN's Ed Werder reported on Sunday that Smith, who was suspended nine games for violating the league's personal conduct and substance abuse policies, did not fulfill the counseling requirements to have his suspension shortened.
NFLPA executive vice president for external affairs George Atallah disputed the report on Monday.
"Aldon fulfilled all of his obligations to be considered to return from his suspension early. The NFL chose not to make that decision."
Smith's agent, Doug Hendrickson, also told Pro Football Talk's Mike Florio that Smith "upheld all requirements" for the league to consider reducing his suspension.
Smith's suspension ended following the team's 27-24 win over the New Orleans Saints on Sunday, and he will be reinstated on Monday.
Since being the No. 7 pick in the 2011 NFL draft, Smith has piled up 42.0 sacks in 43 games. He missed five games last season while undergoing treatment following a DUI arrest.
The 49ers are 5-4 on the season and play at the New York Giants on Sunday.
- Paul Palladino