There were two secrets in the letter Iga Nadeshiko sent to Jiraiya no Sannin. (She called him Jiraiya no Koga in her head- just to herself. But that wasn't the secret, or written down anywhere, so she took it to her grave.)
The secrets were, in order, where his daughters were, and what he had to do to keep them safe.
The dreadful mathematics of necessity being what they are, Nadeshiko forbid Jiraiya from contacting his daughters- forbid him from even admitting he had daughters. He understood why instantly, of course. He hadn't expected a letter from her so soon, honestly- and, in fact, he got two, the first being a summary of all the information she had managed to… "acquire" in her missions for Konoha, all her suspicions and figuring about what was to come- everything he had asked of her, and a great deal more.
Jiraiya got Nadeshiko's letters after her death; the first being a veritable tome of information he had suspected, known, and hadn't known- but seeing it all laid out so neatly made him wonder if he shouldn't consider getting closer to Iga-san, bring her closer to his hand. Her second letter strangled those half-born dreams- and so he was informed, summarily, of the protections she had placed around their children. A secret inside a secret is well hidden indeed- and to anyone who would find that letter, it would appear to be a quietly desperate missive begging for him to watch over a fellow comerade's daughters.
The Sandaime knew about the outer secret- Jiraiya, being the Konoha spymaster, had agents all over the world, and Iga Nadeshiko was one of the very best spies to ever come to, or from, Konoha. It is not so strange, therefore, that she would ask her boss to watch over her children.
He will wonder, later, how he could have been so blind.