Democrats and rights groups have condemned the arrests as "cruel".
Nearly 700 workers from seven agricultural processing plants were arrested for allegedly not having proper documentation to be in the US.
Pictures emerged of children crying after being separated from their parents.
Officials say they took steps to ensure any children were properly cared for.
Immigration and Customs Enforcement (ICE) said "approximately 680 removable aliens" had been detained during the operation, which saw agents arriving in buses to question and arrest workers at the plants.
President Donald Trump had announced an immigration crackdown in June, saying "millions of illegal aliens who [had] found their way into the US" would be removed.
What did ICE say?
ICE spokesman Bryan Cox told the BBC that, of the 680 people arrested in Wednesday's raids, more than 300 had been released with notices to appear before immigration judges.
"They were placed into proceedings before the federal immigration courts and will have their day in court at a later date," he said in an emailed statement.
Those who were not released will be moved to an ICE detention facility and held there, Mr Cox said.
About 30 of the people detained were released on humanitarian grounds, the US Attorney's Office for the Southern District of Mississippi said.
Mr Cox said those arrested were asked if they had any dependents needing care or if they had any children at school who needed to be picked up.
They were given access to phones at the processing site to make arrangements to care for their children. He said those with childcare issues were "expeditiously processed and returned".
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In response to critics who called the raids cruel and harmful to the workers' children, Mr Cox said the agency had directed two Homeland Security Investigations employees to notify schools of the operation and provide contact details for any children whose parents did not pick them up.
"This agency took extensive steps in planning for this operation to take special care of situations involving adults who may have childcare situations or children at school at the time of their arrest."
Those detained had been taken to a Mississippi National Guard hangar for questioning.
ICE did not share details about the nationalities of those detained, but the Mexican government has reportedly sent consular staff to the area to help any of their nationals who may be involved.
What happened at the plants?
The raids took place just hours before Mr Trump arrived in the majority Latino city of El Paso to mark a mass shooting which left 22 people dead.
About 600 ICE agents arrived at the chicken processing plants, owned by five different companies, in the towns of Bay Springs, Canton, Carthage, Morton, Pelahatchie and Sebastopol.
Friends and family looked on as officers surrounded plants and began to arrest the workers.
Nora Preciado, a supervising attorney at the National Immigration Law Center (NILC), told the BBC that, in many workplace raids, "ICE often singles out people in a discriminatory fashion by focusing only on the Latino workers, and there are many incidents of excessive force during the detention and arrests".
"These raids are rife with constitutional rights' violations, including agents having no legal authority to detain or arrest workers based solely on immigration status without probable cause," she said.
"Generally, regardless of whether released or not, anyone unauthorised will be put into deportation proceedings."
In the Mississippi raids, officials said they executed federal criminal and administrative search warrants for the arrested individuals.
What happened to the children?
Some children were taken to a local gym after they came home to find their parents gone.
In one video posted on Facebook from the Koch Foods plant in Morton, a young girl can be heard weeping uncontrollably as bystanders watch people being loaded on to a bus.
An officer allows her to see her mother, who is the girl's only legal guardian, before the buses leave. Because the young girl is a US citizen, her mother will not be deported, the officer says.
According to the Washington Post, the girl's mother had not been released as of Wednesday night.
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Ms Preciado of the NILC said research shows raids like this have a "harmful impact on safety, educational success, social and behavioural well-being and overall health of children in immigrant families".
Scott County schools superintendent Tony McGee told the Clarion Ledger newspaper that one child had started kindergarten on Tuesday, only to have their parent arrested on Wednesday.
Mr McGee said at least six families had a parent detained in the raids, with children ranging in age from kindergarten to high school.
"We'll worry about the school part of it after we get all this sorted out," he added. "You can't expect a child to stay focused on the schoolwork when he's trying to focus on where Mom and Dad are."
What's been the reaction?
Jackson Mayor Chokwe Antar Lumumba condemned the raids as "dehumanising and ineffective".
The American Civil Liberties Union (ACLU) called the operation "unnecessary and cruel".
But Mike Hurst, US Attorney for the Southern District of Mississippi, said ICE agents were executing warrants to arrest the "illegal aliens".
"They have to follow our laws, they have to abide by our rules, they have to come here legally or they shouldn't come here at all," he told a press conference.
Some Trump supporters on Twitter also backed the agency, saying the law must be enforced.
Democratic presidential hopeful Kamala Harris said in a tweet: "These ICE raids are designed to tear families apart, spread fear, and terrorise communities. These children went to daycare and are now returning home without their parents because Trump wants to play politics with their lives."
Fellow 2020 contender Cory Booker echoed the same sentiment.
"The moral vandalism of this administration has no end - how is traumatising these kids, abandoning them, making anyone any safer?"