Yes, you definitely write comments inside methods in Java.

As Sun's code convention says:

Java programs can have two kinds of comments: implementation comments and documentation comments. Implementation comments are those found in C++, which are delimited by /*...*/, and //. Documentation comments (known as "doc comments") are Java-only, and are delimited by /**...*/. Doc comments can be extracted to HTML files using the javadoc tool.

So, the comments in methods are implementation comments.