Al-Assad flew to the Egyptian capital on Tuesday for a visit of only a few hours and immediately went into talks with Mubarak.
Syria has come under increasing international pressure since the UN investigation into a Lebanese leader's assassination in February has accused its government of failing to provide full cooperation.
The investigation, headed by German prosecutor Detlev Mehlis, has exacerbated tensions between Lebanon and Syria.
The Lebanese government welcomed Mehlis' finding that Rafiq al-Hariri, the former Lebanese prime minister, was killed with the complicity of the Lebanese and Syrian intelligence services, but Syria rejected it as unfounded.
After their talks, neither al-Assad nor Mubarak spoke to the media.
Ahmed Aboul Gheit, the Egyptian foreign minister, said they "focused on the main regional issues related to the Mehlis investigation and the latest UN Security Council decision and how Syria dealt with it, as well as Syrian-Lebanese relations and how to advance them".
Last week, the UN Security Council extended the mandate of the investigation by six months.
Al-Sharaa says Syria was beset
by campaigns from abroad
It also said Syria had not yet provided "full and unconditional cooperation" to the inquiry - a charge Syria denied.
Farouk al-Sharaa, the Syrian foreign minister, said Syria was beset by "campaigns from abroad" and there were "internal elements (in Lebanon) who used them and escalated them ... for political purposes".
He did not name the Lebanese opposed to Syria, but he said his government was determined to improve relations with Lebanon.
Referring to the expected appointment of a replacement for Mehlis, who is stepping down this month, al-Sharaa said Syria would "deal in a constructive manner with the new UN investigator and we will offer him every possible help to arrive at the truth".
"We don't want to tell him that such and such happened in the previous investigation - that there were false witnesses whose intentions appeared afterwards and there were biased witnesses with narrow interests in Lebanon who gave statements that do not serve the investigation and the truth," al-Sharaa said.
During the presidents' discussions, Aboul Gheit met with his Syrian counterpart.
Egypt, the political heavyweight of the Arab world, has been trying to mediate between Syria and the West.