From 8 September, the maximum draft of ships will be cut to 39ft (11.89m), which may affect up to 20% of traffic.
A similar restriction was imposed for the same reason in 1998.
The authorities say a further cut in the draft could be imposed on 16 September if the situation does not improve.
The authority has taken the action because water levels in the Gatun and Alhajuela lakes has reduced as a result of the El Nino weather phenomenon.
The current draft limit is 39.5ft, which will be cut to 39ft on 8 September and then potentially to 38.5ft on 16 September.
Shipping companies had been warned the cuts could be coming.
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