The teenager's murder raised tensions amid claims it was in revenge for the killing of three Israeli youths.
Ten Palestinians were injured when Israel carried out air strikes on Gaza early on Thursday, officials say.
Israel's air attacks were in response to mortar and rocket fire from Palestinian militants.
"The Israeli Air Force attacked 15 terror sites in Gaza early Thursday morning," an Israel Defense Forces (IDF) official said.
"The targets included weapons manufacturing sites as well as training facilities," the official added.
Israeli officials said militants had fired dozens of mortars and rockets since Wednesday morning and that two had struck houses in the southern town of Sderot on Thursday. There were no reports of injuries.
They were an immediate response to a wave of attacks from Gaza in which rockets and mortars were fired at southern Israel.
Israeli military sources say the targets were weapons manufacturing facilities and training sites used by [the militant groups] Hamas and Islamic Jihad.
But the exchange of fire comes at a time of rising tension in Israel and the occupied territories.
As the time for the burial approached, the family appeared to accuse the Israeli authorities of holding the body unnecessarily - something denied by police.
Later, Mohammed Abu Khdair's father, Hussein Abu Khdair, said he had been told an autopsy was still taking place. Relatives nevertheless hope the funeral can take place on Thursday.
The post-mortem, which is being conducted by Palestinian and Israeli physicians, is reported to be taking longer because the body was damaged by fire.
In another development, Hussein Abu Khdair said he was held by police for eight hours and put under pressure to say his son's killing was not likely to be an attack to avenge the deaths of the Israeli youths. Police have rejected the claim.
When it does take place, there are fears the funeral will be followed by more clashes like those which erupted outside the teenager's home on Wednesday.
Protesters threw stones at officers, who responded by firing sound bombs, tear gas and rubber bullets.
The Palestinian boy's father said he was told an autopsy was still taking place 
Israel launched air strikes against targets in Gaza on Thursday in response to Palestinian militant mortar attacks 
Two homes were damaged by Palestinian rocket fire in the southern Israeli town of Sderot 
The murder of Mohammed Abu Khdair sparked protests in East Jerusalem on Wednesday His body was later found, bearing marks of violence, in West Jerusalem.
Palestinian President Mahmoud Abbas accused Jewish settlers of killing the boy, calling for the "strongest punishment against the murderers".
Israeli Prime Minister Benjamin Netanyahu said the murder was "despicable" and that he had ordered police to work "as quickly as possible to find out who was behind the heinous murder of the youth".
Two cousins of Mohammed Abu Khdair spoke to Yolande Knell about his death
Dan Margalit in free, pro-Netanyahu Yisrael Hayom: ""Certainly every decent Israeli wants to get rid of the murderers of Eyal Yifrach, Naftali Fraenkel and Gilad Shaer. There is a blood debt with the two Palestinians who murdered them...the IDF and the Shabak must hunt them, not wild groups who operate outside public life."
Pro-Fatah Palestintian daily Al-Quds: "We say once again that peace is the only way leading to the suspension of violence, fanaticism and tension."
Dr Isam Shawir in Hamas-run, Gaza-based Filastin: "The threats made by the occupation are worthless and do not scare Hamas, particularly in the Gaza Strip."
"If the Arab youth was murdered because of nationalistic motives, then this is a horrible and horrendous act," the statement from the family of Naftali Frenkel said.
Israeli police have urged caution over the motives for the killing, saying they are still investigating.
The bodies of the three Jewish seminary students were found near the city of Hebron on Monday, two-and-a-half weeks after they were abducted. Their funerals took place on Tuesday.