The League Two club were facing their sixth in four years having been issued with the petition by HMRC two weeks ago.
The Shrimpers are due in the High Court for their hearing on June 24, when the case will be dismissed.
Southend finance director Nigel Brunning told the club's official website: "This tax was for one month's PAYE/NIC and was three days overdue when HMRC served notice.
"The past four and three quarter years since the banking crisis have been challenging times for many companies and the club is no exception.
"Following relegation from the Championship in 2006/07 the club incurred significant losses, which we have been able to improve year on year since then. That trend is forecast to continue into next season. The club's parent company have been supportive throughout and again advanced the funds to discharge the liability to HMRC.
"As the financial position continues to improve it is hoped the club will become less dependant on its parent as it moves into the new stadium."