Colchester will have to pay Dagenham an initial £45,000 for defender Magnus Okuonghae.
A Football League tribunal has also ruled that the figure could rise to £80,000 depending on appearances and whether the Us are promoted in the next two seasons.
"The process was productive and the whole procedure was run very professionally," said Colchester chief executive Steve Bradshaw.
"It feels like a fair reflection of his value given the fact that, while having been very impressive last season, it was his first full league campaign from start to finish."
Okuonghae, 23, enjoyed an impressive debut for the Us on Saturday as they ran out 7-1 winners at Norwich.
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