But Kushner, Trump's senior adviser and son-in-law who had no government or diplomatic experience before taking office and recently lost his top-secret security clearance, has been criticized for not including the outgoing U.S. ambassador in his meetings.
The meetings with Pena Nieto and Mexican Foreign Secretary Luis Videgaray come at a critical but fraught time in U.S.-Mexican relations. Two weeks ago, Trump and Pena Nieto were speaking on the phone about the Mexican leader’s finally visiting the United States when Trump went off script and brought up the wall, according to two senior administration officials.
Pena Nieto said Mexico would not support the wall, while Trump reiterated his campaign position that it would. Both sides then concluded that now was not the right time to move forward with a visit, according to one of the officials.
After Wednesday's meetings, however, it appeared there had been little progress in rescheduling. Mexican officials say both sides agreed that a future meeting will depend on how much progress is made on other issues, including NAFTA, migration, economic cooperation, and security, which would include Trump's proposal for a border wall.
The White House has not yet released its own statement. But Kushner brought Trump's message about the importance of continuing to work together on joint initiatives, and both countries agreed to work together to achieve positive results for both sides, according to Mexico.
U.S. Ambassador Roberta Jacobson, a 30-year veteran of U.S.-Latin America policy and top diplomat who has announced her resignation, was not in either of Kushner's meetings with Videgaray or Pena Nieto, according to a statement and photos released by the Mexican government. She was also not even invited, according to The New York Times.
The State Department has not yet commented on the issue.
While Jacobson was absent, Kushner did have with him Kimberly Breier, Trump's pick to be the top diplomat for North and South America. Breier is a member of the State Department policy planning staff and was announced Monday as the administration's nominee for assistant secretary of state for Western hemisphere affairs.
That role, like many other top positions at the State Department, is vacant. The bureau is led by Francisco "Paco" Palmieri, an esteemed senior Foreign Service officer who is the principal deputy assistant secretary. Breier must be confirmed by the Senate before she can assume the role.
Jacobson is resigning her position and leaving the State Department in May, she announced last week.
It's the third big departure among the agency's Latin American experts: The third-highest ranking official, Under Secretary of State for Political Affairs Tom Shannon is retiring and will leave after a replacement is announced. U.S. Ambassador to Panama John Feeley will leave his post Friday after submitting his resignation in January in a letter to staff about how he could no longer serve Trump.
ABC News's Jordyn Phelps and Kirit Radia contributed to this report.