The environmental tax was announced as part of a USD 32 billion budget for the 2014-15 fiscal year, which also focused on giant new infrastructure projects such as a metro in the cramped capital Dhaka and a nuclear power plant to boost growth.
Industrial effluent and waste from urban sewage "is severely contaminating our rivers and taking heavy toll on the aquatic environment and its surroundings", Finance Minister A.M.A Muhith said as he announced the budget in parliament.
A revenue official told AFP the tax would be imposed on a company's turnover if it is found to have polluted "air, soil and water".
Muhith also announced tax exemptions for the country's 6,000 brick factories if they build environmentally friendly kilns.
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The budget is the first since Prime Minister Sheikh Hasina's centre-left government was re-elected in January polls marred by widespread fraud and a boycott by opposition parties.
Factories currently face one-off fines if they are found in breach of pollution standards, but bosses often bribe inspectors to turn a blind eye.
The new tax would mostly affect the powerful textile and leather processing industries that often pour untreated effluent straight into the country's rivers.
There are around 200 hide-processing factories based in the Hazaribagh district of Dhaka, listed as the world's sixth most polluted place by a environment group, but none of them have effluent treatment plants.