The A23 and the B2110 at Pease Pottage, West Sussex were closed for several hours on Wednesday after an Army bomb disposal team was called in.
The Highways Agency said on Thursday the package was a bat box being used as part of a wildlife survey.
It was placed on a bridge over the road in advance of an A23 expansion scheme.
"We are working on ways to improve identification of our property to avoid a repeat of the incident," said a spokesman.
The alert was raised amid fears the bat box contained explosives.
Several homes were evacuated and motorists experienced long delays.
A Sussex Police spokesman said: "As a result of a well-intentioned call by a member of the public the package was investigated but found to be harmless."
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