Minister of economic development Basil Rajapaksa said the proposed 50 US dollar per person fee might be lower for visitors from member countries of the South Asian Association for Regional Co-operation (SAARC).
"Many countries have different (visa) categories," he told a news conference.
"Especially when they are in regional co-operation (arrangements) always they have a special facility - so for SAARC countries it might be something different than for others," he said.
"We are now having the trial run. Anyone can login and apply for a visa before they leave home. The final visa fee is not yet decided and we're still having discussions on it."
Rajapaksa's remarks came after reports that India had asked for a lower fee citing the island's obligations under the SAARC regional trade deal.
Sri Lanka has proposed a 50 US dollar per person fee for the new electronic visa.
Media reports said the Indian High Commission (embassy) in Colombo has raised the issue with Sri Lanka immigration officials last week.
Until the end of this year Indians are allowed in visa on arrival and India now only charges 650 rupees per visa from Sri Lanka unlike Sri Lanka's proposed 5,500 rupee equivalent.
Rajapaksa said the new system was being tested now and was aimed at getting visitors to apply for visas before leaving their home countries.
"We are not much concerned about the visa fees. This is a way of encouraging tourists to get visa before they leave. At present with on-arrival visa, sometimes when a person comes here, at the immigration counter he can be rejected. So in future that will not happen."
