Secret messages are accessible within the game by entering specific passwords:

Password = Message
•Minori Kumiko Kiyoharu = Actually, Erika is Minori! And Minori is a/the older sister!
•Grilled meal = We never want to work all night again. -Iwata and Yamagishi
•Mommy, the company is scary. = I'm honestly not a mama's boy! I'm just a bit spoilt, you see. -Udopyu
•Oomachi in love = I can't express these feelings of mine. I want to tell you, even if it's just a little bit. I love you... -T.O
Contributed by MehDeletingLater
The last characters of the first two five-character segments and the third character from the third segment used as passwords throughout the game spell out a message:

 1章:かきかか かかかか かかみあ ひそそささ
 2章:かけかか かかかか かこみあ ひつたちけ
 3章:かちかき かかせか かさみあ ひちたそす
 4章:きちかけ かこそか かさみあ ひてきそと
 5章:ちちかけ かこそか かさみあ ひとなつく

 1章:かきかか かかかか かかみあ ひてちたす
 2章:かけかか かかかか かこみあ ひつなたす
 3章:かちかき かかせか かさみあ ひてとつそ
 4章:きちかけ かこそか かさみあ ひととちち
 5章:ちちかけ かこそか かさみあ ひつちちし

いいか みてろ きさま いまに ころす
やめた こんな やつら はやく うせろ
Right then! Just you wait! I'll kill you right now!
I changed my mind. Hurry up and get out of here!
Contributed by MehDeletingLater
After the game's ending plays, there are several things that will happen if the game is left running, and it's possible to trigger a hidden message from a programmer named Hidemushi. First, the ending photo will change to black and white after waiting 18 minutes, and then sepia after another 18 minutes. After 55 more minutes, the music will then stop, and pressing A + B + Start + Select + Left on Controller 1 and A + B + Right on Controller 2 will cause some new music to play. Pressing B + Select + Right on Controller 1 and B + Right + Down on Controller 2 will start Hidemushi's message, calling out everyone that he had to put up with while developing the game and thanking those who did help him. Once Hidemushi's message stops, press A + B + Up on Controller 1 for his last message, a dedication to his wife. After waiting 18 more minutes, the game goes back to the title screen.

Two exclusive songs play during this hidden message. The first track is a remix from The Karate Kid NES game, while the other track is completely new and starts playing when the message 「そういえば せわになった ひともいたな・・・・・」 appears, translated in English to "Come to think of it, some people were helpful to me, too." Both games were composed by Hirohiko Takayama. Both songs, unlike the rest of the game, use the Famicom's basic onboard audio system rather than the Namco 163 audio expansion chip which supports up to 8 additional channels.
Contributed by gamemaster1991