Members of the Movement for the Actualisation of a Sovereign State of Biafra (MASSOB) attacked at least seven officials in the market town of Onitsha in Anambra state on Wednesday, the second day of the census in Africa's most populous country.
Uzor A Uzor, of the human rights group the Civil Liberties Organisation, said: "I counted at least seven enumerators who came to report at the police station yesterday that they were attacked with acid."
One of the victims, Felicia Nwachukwu, said three MASSOB members on a motorbike sprayed acid on her back and attacked a colleague with machetes before speeding off.
"We were numbering houses when they came and poured acid on me and slashed my colleague's hand," she said.
In the neighbouring state of Enugu, five census-takers were beaten or macheted and one car was burnt out by MASSOB members trying to stop people from being counted, police and victims said.
There were reports of intimidation of census officials and residents by members of the group in other southeastern states.
MASSOB is campaigning for the southeast, dominated by the Ibo tribe, to become an independent state under the name Biafra. The group says the Ibo, Nigeria's third-biggest ethnic group, should not be counted in the census because they are Biafrans and not Nigerians.
"We were numbering houses when they came and poured acid on me and slashed my colleague's hand"
At least six MASSOB activists were killed in a clash with police on Tuesday after they tried to stop people from being counted in the town of Nnewi in Anambra state.
Elsewhere, the five-day census, which runs until Saturday, was being hampered by logistical problems.
The count did not start on time in many parts of the country because census-takers complained that they had not been paid or had not received sufficient materials.
Censuses are fraught in Nigeria because rival ethnic and religious groups have tried to use them to assert their numerical superiority and claim a larger chunk of oil revenues and political representation.
Five people were killed in southwestern Ondo state last weekend in fighting linked to the census between two ethnic groups over ownership of a village.