In general, not really. While both are queueing solutions, you will find that Windows Azure queues don't have the same guarantees that MSMQ will have (for good reason). For instance, WAQ supports a delivery model of 'at least once' versus 'exactly once'. It also uses a 2PC model where you must pop and then delete a message. It is also not involved in transactions like MSMQ can handle. However, for cloud queuing scenarios, some of these considerations matter less. There are other nuances as well (message TTL, invisibility, renewals, storage time, etc.) that differ.
It might be easier to answer more completely if you explain what features your queueing needs must have. Also, keep in mind that AppFabric has a queueing service that also might be appropriate depending on what you really need.