Thousands of messages were sent to his constituency e-mail inbox urging him to support a European ban on a pesticide linked to the decline of bee populations.
Mr Paterson, who is also the environment secretary, fears that the bombardment on the issue might stop him seeing urgent mail from constituents.
He said: "Everyone has a right to express their view and write to me but this is a cyber attack on the constituency office.
"The danger is that someone may have a real problem, they might need an urgent operation or someone abroad might need help or there could be a crisis in business and if they have sent an e-mail it might not be able to get through.
"I have already had people not able to get through.
"There are real people in North Shropshire writing to me by e-mail.
"It is wrong that they should not get access to the e-mail system."
The bee-related e-mails were a result of a vote on European Commission proposals to restrict the use of neonicotinoids, the pesticides that have been blamed for declines in bee numbers across the world.
The proposals failed to get a majority in the EU vote, from which the UK abstained.
MPs have been told that tests showed bees may be significantly affected by the pesticides but field data on honey bees indicated their level of exposure in real life does not lead to harmful effects.
As a result the Department for Food and Rural Affairs, which Mr Paterson heads, has commissioned field trials on bumble bees with results expected back in the next few weeks.
Mr Paterson said he wanted to wait until the field studies were completed before he made his decision.
"I am not going to be rushed," he said.
"I am really determined to do the right thing for bees.
"People have their right to express their views but 80,000 e-mails is a cyber attack."