A recent Wired article discusses the impact of biometric passports on the operations of intelligence agencies. The problem is that with such passports, it is much harder for a spy to assume a new identity (as the identity is linked to a biometric property). Moreover, hotels typically scan the passport of all guests checking in. This data can be cross-checked in real-time with data gathered at the border crossing and entered in immigration databases to see whether a guest officially entered the country, or whether his passport data appears to have changed in the meantime.
The following quotes make very clear that intelligence agencies will stop at nothing to prevent detection of this (and by extension, for anything else).