The Bostick League Premier Division side have paid an exemption fee as per the competition rules.
Suffolk FA County Cup Competitions Manager Adrian Moye said: “I’m disappointed that Lowestoft Town have felt it necessary to withdraw from the Premier Cup.
“I try to encourage all teams at every level to participate in our County Cup Competitions but there is an exemption fee in our rules and Lowestoft Town have chosen to take that route rather than to participate.
“It’s a real shame because they have been one of the county’s most successful clubs in recent years.”
Needham Market defeated Lowestoft 3-2 in last season’s final at Colchester United FC, to deny the Trawlerboys a third successive victory in the competition.
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