The survey by polling firm Buendia & Laredo for newspaper El Universal said approval of Pena Nieto's performance had fallen to 25 percent from 29 percent in July, hurt by discontent about the economy, rising violence and failure to battle corruption.
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Pena Nieto's six-year term concludes at the end of November 2018, and opinion polls show his centrist Institutional Revolutionary Party (PRI) faces an uphill battle to retain power after the next presidential election, scheduled for July 2018.
Mexican law bars the president from seeking re-election.
The government is scrambling to head off the risk of an economic shock from the election of Trump, who has pledged to isolate Mexico behind a border wall, and threatened to impose steep tariffs on Mexican goods and tear up a joint trade deal.
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To try and create some leverage, Pena Nieto's government hosted Trump for talks on August 31. However, the hastily-arranged visit was staged with scant input from the cabinet and created the impression it was realised on Trump's terms.
Some 66 percent of respondents said Pena Nieto had made a mistake in inviting Trump because he had offended Mexicans in the election campaign. Only 30 percent believed it was a wise move that furthered Mexico's interests, the survey showed.
When asked what was the "worst thing" Pena Nieto had done, seven percent of respondents cited the meeting with Trump, the third most common answer. Only his reforms (12 percent), and failing to battle crime (nine percent) were cited more often.
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The November 11-15 survey polled 1,000 permanent residents of Mexico and yielded Pena Nieto's lowest approval rating from Buendia & Laredo since he took office in December 2012.
Trump sparked outrage in Mexico when he launched his bid for the presidency last year by accusing the country of sending rapists and drug runners north as illegal immigrants.
Pena Nieto's close aide Luis Videgaray, who government officials said was the architect of the meeting, stood down as finance minister a week after Trump's trip. The president himself later conceded the visit could have been handled better.
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