We are often asked by customers how secure it really is to synchronize their passwords to and from Azure AD, be it standalone or as part of Office 365.

Our short answer:

The passwords themselves are never sent over the wire in either direction. In all cases only password hashes are sent.

The longer answer is easily derived and supported both from TechNet articles and various third-party sites. The key take-away is that only the hashes are ever retrieved, additional encryption applied, and then that is sent to Azure AD or back.  The passwords themselves are never used or sent.

From TechNet:

The Active Directory Domain Service stores passwords in form of a hash value representation of the actual user password. The Password hash cannot be used to login to your on-premises network. It is also designed so that it cannot be reversed in order to gain access to the user’s plain text password. To synchronize a password, the Directory Sync tool extracts the user password hash from the on-premises Active Directory. Additional security processing is applied to the password hash before it is synchronized to the Azure Active Directory Authentication service.

When synchronizing passwords using the password sync feature, the plain text version of a user’s password is neither exposed to the password sync tool nor to Azure AD or any of the associated services.

Additionally, there is no requirement on the on-premises Active Directory to store the password in a reversibly encrypted format. A digest of the Windows Active Directory password hash is used for the transmission between the on-premises AD and Azure Active Directory. The digest of the password hash cannot be used to access resources in the customer's on-premises environment.

https://technet.microsoft.com/en-us/library/dn246918.aspx

From A Third-Party

An independent company that makes SharePoint and Office 365 tools also performed their own analysis, down to the packet capture level. What they found was:

The hash over the wire that is captured is not an MD4 hash of clear text password. It is a secure PBKDF2 key derived from SHA256 hash of the MD4 hash (derived from crypto API documented at http://msdn.microsoft.com/en-us/library/windows/desktop/dd433795(v=vs.85).aspx) per RFC 2898.

Read more at their blog post:
https://www.cogmotive.com/blog/office-365-tips/how-secure-is-dirsync-with-password-synchronisation

Overall we're very confident using this functionality at our customer deployments, and Microsoft have created a well thought out and secure implementation.