The stoppages happened after needles were thrown into green recycling bins and ended up on a conveyor for sorting.
Each stoppage may last only a few minutes, but staff estimate that the plant lost a week's productivity because of the problem last year.
Only one of the 20 sorters has been pricked by a needle and was tested negative for infections like HIV.
An emergency bell is rung each time a needle is spotted and disposed of in a special container.
More than 2,100 needles were collected last year and figures indicate that there will be just as many disruptions this year.
Cleansing manager Simon Hill said: "We can't recycle needles, but more seriously there's a real risk that our staff could be injured from one of these discarded needles because they are working by hand."
The city council's street cleaners and gardeners are picking up about 50 used needles a day.
The council is now working with the Devon Drug and Alcohol Action team to improve free collections in the hope that needle users, both medical and recreational, will be more responsible.
Councillor Rob Hannaford said: "There's an economic cost because it is making the service more expensive to the taxpayer because of lost productivity.
"More seriously it is a source of concern to our staff because they never know when a used hypodermic needle is going to suddenly appear in front of them."
Discarded hypodermic syringes brought Exeter's rubbish recycling plant to a halt 869 times last year.