[anrakushi]

this is not a problem with just Japanese, it is a problem with all languages, i can assure you as someone who has spent a lot of time teaching english to students in melbourne that these same problems exist for learners of english.

im used to using either 辞典 or 辞書 for just saying dictionary. there are these examples for when you are referring to more specific things.
電子辞書　でんしじしょ　electronic dictionary
英和辞典　えいわじてん　English-Japanese dictionary
漢和辞典　かんわじてん　Chinese-Japanese character dictionary

also i believe 字典 - this is more of a character dictionary. i'm sure nagoyankee or MMM can come along and shed some light on when to use each one, but my guess is that they are interchangeable except for the above examples.