They did come under judgment—but not immediately, and not in the same way Israel was judged. Scripture shows several reasons:

1. The Ark’s Capture Was God’s Judgment on Israel, Not a Victory of the Philistines

Israel’s sin and rebellion brought about the loss of the ark.
The LORD had already pronounced judgment on Eli’s house (1 Sam. 2:27–36; 3:11–14).

So the ark’s capture was:

• God disciplining His own people, not the Philistines winning a triumph.

• A fulfillment of His word that Hophni and Phinehas would die on the same day (4:11).

God was judging Israel’s sin first—because judgment begins at the house of God (cf. 1 Pet. 4:17, a general principle also true in the OT).

Thus, the Philistines were instruments of His discipline at that moment.

2. God Allowed Time for the Philistines to Exalt Themselves—So He Could Publicly Humiliate Their False Gods

If God had immediately struck the Philistines dead the moment they touched the ark:

• There would have been no public demonstration of the powerlessness of Dagon.

• The Philistines might have attributed the deaths to coincidence, plague, or war.

Instead, God did something far greater:

He destroyed Dagon on his own altar (1 Sam. 5:3–4).

Dagon fell before the ark.
Then his head and hands were cut off.

God made it unmistakable that:

• The LORD alone is God.

• The gods of the Philistines were nothing.

This was a public testimony to the heathen nations, not just to Israel.

3. God Did Judge the Philistines—but Gradually and Specifically

1 Samuel 5 makes it clear:

• “The hand of the LORD was heavy upon them” (5:6).

• He “destroyed them” and “smote them with emerods” (5:6).

• In Ekron, “there was a deadly destruction” (5:11).

• “The cry of the city went up to heaven” (5:12).

God did not spare them—He simply did not annihilate them instantly.

The judgment was:

• Progressive

• Escalating

• Unmistakably supernatural

The result?
The Philistines themselves begged to send the ark away.

4. God Intended to Teach Both Israel and the Philistines the Same Lesson: His Holiness

When the ark arrived at Beth-shemesh, the Israelite men who looked into the ark were struck dead (6:19).
The same God who judged pagans for disrespect judged Israelites even more severely when they should have known better.

This reinforces a central biblical truth:

Greater light brings greater responsibility.

Israel had:

• The Law

• The priesthood

• The tabernacle

• The sacrifices

• The covenant

They knew the holiness of God.
The Philistines did not.

Thus, God’s judgments are always consistent with His holiness and the level of revelation each group had received.

5. God Used the Event to Bring Israel to Repentance (1 Samuel 7)

If the Philistines had been instantly destroyed, Israel might have:

• Returned to superstition

• Continued in sin

• Assumed the ark itself had mystical power

Instead, the long return of the ark provided:

• Time for conviction

• Time for national sorrow

• Time for Samuel’s spiritual leadership to take hold

This culminated in the great revival at Mizpeh (1 Sam. 7:3–6).

Summary

The Philistines were not immediately killed for several reasons:

1. The ark’s capture was God’s judgment on Israel first.

2. God wanted to publicly humiliate Dagon and expose Philistine idolatry.

3. God did judge the Philistines, but progressively and purposefully.

4. Israel, having greater knowledge, bore greater responsibility.

5. The whole event prepared Israel for national repentance and revival.

God’s actions were not random—He was teaching both nations about His holiness, sovereignty, and truth.