Amnesty International said that at least 28 people of over 100 arrested have been convicted in connection with the protests.
The opposition are calling for incumbent Faure Gnassingbe to immediately step down as president.
Wednesday's clashes came on the back of violent scenes in the northern town of Sokode where state agents reportedly arrested an Imam who is closely allied to an opposition chief, Tikpi Atchadam.
The violence has spread to several other cities in the north as well as Lome.
"Security forces aren't the only ones in possession of weapons, so it's hard to say who fired", security minister Colonel Yark Damehame told reporters.
The heavy police presence in Lome to enforce a government ban on weekday marches failed to subdue the demonstrators, who tried to erect barricades across the capital, while shops and businesses remained closed.
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"The assembly points have been taken over by the security forces", said Eric Dupuy, spokesman for the main opposition National Alliance for Change (ANC).
On Tuesday, two teenagers and two soldiers were killed during clashes in Sokode that followed the arrest of a local imam who is close to the PNP. But he added: "We are going to march whatever the cost and intimidation".
The protesters are demanding a return to the 1992 Constitution of Togo, which limits presidency terms.
The referendum is to be held in the coming months but the opposition has complained that the new measures are not retroactive.
The president won elections in 2005, 2010 and 2015. Gnassingbe would thus be eligible for two further five-year terms under the terms of the proposed bill, leaving him in power until 2030.
They say they want an end to a family dynasty that has ruled the West African nation for the last fifty years.
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