Businesses, including fast-food chains, were shut in support of the protest.
President Otto Perez Molina is facing impeachment proceedings over the affair, which has seen his former deputy Roxana Baldetti jailed and six cabinet ministers quitting in protest.
He has apologized over the scandal but denies involvement. He is due to step down at the end of his term in January.
Guatemalans are due to vote in just over a week’s time to choose his successor.
Investigators have alleged that top government officials received a cut from bribes paid by businesses seeking to evade import duties.
The scandal has been dubbed “La Linea”, or “The Line”, after the hotline businesses allegedly rang to clear their imports through customs at cut-price rates.
UN-backed investigators have accused Otto Perez Molina of direct involvement in the customs scandal.
In a televised address to the nation last week, the president dismissed the allegations and insisted that his conscience was clear.
Former VP Roxana Baldetti has been arrested over her alleged involvement in the affair.
Prosecutors say she took a 50% cut from the bribes. She appeared in court on August 26, denying the charges.
On August 27, marchers took to the streets of Guatemala City, waving placards attacking corruption in the political establishment.
A committee has meanwhile been formed to consider lifting the president’s immunity from prosecution.
The committee was created after Guatemala’s Supreme Court gave the go-ahead for prosecutors to request impeachment proceedings.
Major business and religious leaders are supporting calls for President Otto Perez Molina to resign.
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