The League Two club are now facing their sixth in four years over an unpaid tax bill and will go to court on June 24.
The Shrimpers were last facing a petition by HMRC as recently as March when the debt was paid.
Southend are declining to make an official comment on the matter.
The Essex club finished 11th in League Two this season and were Johnstone's Paint Trophy finalists, losing 2-0 to Crewe at Wembley.
- Sports & Recreation