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Hi, lamyo,
We bought an apartment last year (state capital, different state), and this doesn't track our experience at all:  ITBI (I'm assuming that you're talking about the Real Estate Transfer Tax, because I'm not familiar with an "ITBE") was based on our purchase price.   Did you pay a market price for the apartment, or have some kind of special deal?   This is the only case I can think of where the tax might be based on a higher amount.
In your place, my first stop would be at the Cartório that processed/is processing the paperwork (Escritura) for the sale; they should be able to explain the difference.
If they can't, or you're not satisfied with the explanation, the Prefecture's web page on the tax is here:

Their Taxpayer Services office is here:
Palácio Jerônimo Monteiro
Avenida Marechal Mascarenhas de Moraes, 1.927, Bento Ferreira
I suppose that this would be my next stop.  Good luck!

The assessed tax is , in most cases, based upon the "valor venal", or assessed value by the city upon which said property is under jurisdiction. 

The only other tax which does not strictly follows "valor venal" is the transfer tax or ITBI. On this particular case,  the levied tax is based on whichever value is the highrest, whether it is the Venal or the Negotiated Purchase Price.

In most muncipalities the "valor venal" is way lower than the market value of the property upon consideration.

Trying to challenge the City's declared "Valor Venal " is an exercise of futility, a waste in attorney's fees and your time, unless the "Valor Venal" far exceeds the Market Value.

We had this to take place in Santo Andre, but then, a protesting march was organized and the City receeded in their stance ( call it an organized protest with political consequences to elected officials ).  Whoever then paid the higher tax value will only see a credit towards next year's tax bill.  That City is Santo Andre, SP.

If you are a lone ranger trying to fight off the fairness of Tax Assessor's Office, well, you are in for a big surprise.

Our experience was in line with sprealestatebroker's description.   Our purchase price was higher than the "valor venal", and the ITBI ended up based on it, although we weren't sure which value the Prefecture would use until they processed the transaction.
We're now waiting for our IPTU documents for this year, and expect to see that the "valor venal" has been adjusted upward to match.