Socialist Axelle Lemaire said it was "clearly tactical" for the European Commission president to suggest it would be "difficult if not impossible" for an independent Scotland to join the EU.
The deputy - dubbed the "MP for Paris-on-Thames" because her northern Europe constitency includes so many British-based voters - is just the latest continental politician to question Mr Barroso's remarks, made on the BBC's Andrew Marr Show last month.
Visiting Scotland, Ms Lemaire said: "It is extremely important to remain neutral and respect the independence debate.
"President Barroso of the European Commission got involved in the debate and give his view on behalf of the member states, which haven't said anything. I thought it was not correct.
"It is clearly tactical because he wants to become secretary general of Nato and he thinks that having the support of Britain for the nomination is a good thing. I take the opposite view, which is that I should not get involved."
Brussels spin doctors sought to qualify Mr Barroso's remarks almost as soon as he made them, especially his comparison of Scotland with the former Serbian province of Kosovo, which has never been recognised by anti-separatist states such as Spain or Ukraine.
Earlier this month Joelle Garriaud-Maylam, a senator from the opposite side of French politics from Ms Lemaire, also attacked the EC president.
Speaking in the Senate, she said: "The threats formulated by Mr Barroso are inappropriate and the result of Spanish and English pressure. London is increasingly worried. They (the threats) are not credible. If Scotland votes for independence, it will stay in the European Union. It would be in England's interest."
Mr Barroso has never formally expressed a desire to become Nato general secretary when his term as EC president ends this year. He has been widely linked with the job, however.
Ms Lemaire, meanwhile, said Scotland's French community - 7000 were recorded in the last census in 2011 - were divided on the referendum.
She said: "My constituents are completely split. Many of them are dual nationals so they have a variety of positions, and are just as diverse as Scots are.
"The referendum is only not for British people, not only for Scots. It is for anyone who decides to live here and wants to contribute. It amazes me how passionate people are, on both sides, and it seems to be a grassroots debate.
"The way the debate is taking place is setting an example for the rest of the world, especially when you compare it with places where people are fighting."